Improving macromolecular structure refinement with metal coordination restraints - examples

This archive contains re-refined macromolecular structures presented in manuscript "Improving macromolecular structure refinement with metal coordination restraints" written by Kaveh H. Babai, Fei Long, Martin Malý, Keitaro Yamashita and Garib N. Murshudov and published in Acta Crystallographica Section D. The JSON files describing metal coordination were generated using MetalCoord. These JSON files were converted to restraints using the included script json2restraints.py . The structures were re-refined in Servalcat using updated monomer dictionaries for metal containing ligands. Used commands: 1w9m metalCoord stats -l FS2 -o 1w9m_FS2_mc.json -p 1w9m.pdbmetalCoord stats -l SF4 -o 1w9m_SF4_mc.json -p 1w9m.pdbpython3 json2restraints.py -i 1w9m_*_mc.json -o 1w9m_mc_restraints -p 1w9m.pdb servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m_mc_restraints.pdb -s xray --ligand SF4_metalcoord_refined_updated.cif FS2_metalcoord_refined_updated.cif --keyword_file 1w9m_mc_restraints.txt -o 1w9m_serval_corrlibrary_restraints > 1w9m_serval_corrlibrary_restraints.log servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m.pdb -s xray --ligand SF4_metalcoord_refined_updated.cif FS2_metalcoord_refined_updated.cif -o 1w9m_serval_corrlibrary_norestraints > 1w9m_serval_corrlibrary_norestraints.log servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m.pdb -s xray -o 1w9m_serval_oldlibrary_norestraints > 1w9m_serval_oldlibrary_norestraints.log 2ynm metalCoord stats -l AF3 -o 2ynm_AF3_mc.json -p 2ynm.pdbmetalCoord stats -l SF4 -o 2ynm_SF4_mc.json -p 2ynm.pdbmetalCoord stats -l PMR -o 2ynm_PMR_mc.json -p 2ynm.pdbmetalCoord stats -l MG -o 2ynm_MG_mc.json -p 2ynm.pdbpython3 json2restraints.py -i 2ynm_*_mc.json -o 2ynm_mc_restraints -p 2ynm.pdb gemmi cif2mtz 2ynm-sf.cif 2ynm-sf.mtzservalcat refine_xtal_norefmac --adp iso --hklin 2ynm-sf.mtz --model 2ynm_mc_restraints.pdb -s xray --free 0 --ligand PMR_servalcat_updated.cif SF4_servalcat_updated.cif AF3_servalcat_updated.cif --keyword_file 2ynm_mc_restraints.txt -o 2ynm_serval_corrlibrary_restraints > 2ynm_serval_corrlibrary_restraints.log 4dl8 metalCoord stats -l AF3 -o 4dl8_AF3_mc.json -p 4dl8.pdbmetalCoord stats -l MG -o 4dl8_MG_mc.json -p 4dl8.pdbmetalCoord stats -l NA -o 4dl8_NA_mc.json -p 4dl8.pdbpython3 json2restraints.py -i 4dl8_*_mc.json -o 4dl8_mc_restraints -p 4dl8.pdb servalcat refine_xtal_norefmac --hklin 4dl8-sf.cif --model 4dl8_mc_restraints.pdb -s xray --ligand AF3_servalcat_updated.cif --keyword_file 4dl8_mc_restraints.txt -o 4dl8_serval_coorlibrary_restraints > 4dl8_serval_coorlibrary_restraints.log 6i3j metalCoord stats -l FC6 -o 6i3j_FC6_mc.json -p 6i3j.pdbmetalCoord stats -l CU -o 6i3j_CU_mc.json -p 6i3j.pdb -c 3metalCoord stats -l NA -o 6i3j_NA_mc.json -p 6i3j.pdbpython3 json2restraints.py -i 6i3j_*_mc.json -o 6i3j_mc_restraints -p 6i3j.pdb# manual edit of 6i3j_mc_restraints.pdb to delete a wrong LINK between sodium and carbon atoms: 6i3j_mc_restraints_edit.pdb# manual edit of 6i3j_mc_restraints.txt to delete wrong restraints for sodium atoms A620 and B620: 6i3j_mc_restraints_edit.txt# manual merge of the dictionary FC6.cif with the dictionary for TRP-HIS covalent bond: FC6_metalcoord_refined_updated_TRP-HIS.cifservalcat refine_xtal_norefmac --hklin 6i3j-sf.cif --model 6i3j_mc_restraints_edit.pdb --d_min 2.59 -s xray --ligand FC6_metalcoord_refined_updated_TRP-HIS.cif --ncsr --keyword_file 6i3j_mc_restraints_edit.txt -o 6i3j_serval_corrlibrary_restraints --vonmises > 6i3j_serval_corrlibrary_restraints.log 6wj6 metalCoord stats -l CLA -o 6wj6_CLA_mc.json -p 6wj6.cif -c 5metalCoord stats -l HEM -o 6wj6_HEM_mc.json -p 6wj6.cifmetalCoord stats -l FE2 -o 6wj6_FE2_mc.json -p 6wj6.cifpython3 json2restraints.py -i 6wj6_*_mc.json -o 6wj6_mc_restraints -p 6wj6.cif# manual edit of 6wj6_mc_restraints 6wj6 in Coot: 6wj6_mm01.mmcif servalcat refine_spa_norefmac --model 6wj6_mm01.mmcif --map emd_21690.map --source electron -d 2.58 --ncsr --ligand CLA_servalcat_updated.cif HEM_servalcat_updated.cif --keyword_file 6wj6_mc_restraints.txt -o 6wj6_mm01_serval > 6wj6_mm01_serval.log 3ayf metalCoord stats -l CA -p 3ayf.cif -o 3ayf_CA_mc.jsonmetalCoord stats -l HEM -p 3ayf.cif -o 3ayf_HEM_mc.jsonmetalCoord stats -l ZN -p 3ayf.cif -o 3ayf_ZN_mc.json # using the trigonal-bipyramid geometry class for zinc (lowest procrustes score):python3 json2restraints.py -i 3ayf_CA_mc.json 3ayf_HEM_mc.json 3ayf_ZN_mc.json -o 3ayf_restraints_mc -p 3ayf.cifservalcat refine_xtal_norefmac --hklin 3ayf-sf.cif --model 3ayf_restraints_mc.mmcif -s xray --ligand HEM.cif --keyword_file 3ayf_restraints_mc.txt -o 3ayf_serval_corrlibrary_restraints # using the square-pyramid geometry class for zinc - after manual edit of 3ayf_ZN_mc.json to 3ayf_ZN_mc_SqPyr.json:python3 json2restraints.py -i 3ayf_CA_mc.json 3ayf_HEM_mc.json 3ayf_ZN_mc_SqPyr.json -o 3ayf_restraints_mc_ZnSqPyr -p 3ayf.cifservalcat refine_xtal_norefmac --hklin 3ayf-sf.cif --model 3ayf_restraints_mc_ZnSqPyr.mmcif -s xray --ligand HEM.cif --keyword_file 3ayf_restraints_mc_ZnSqPyr.txt -o 3ayf_serval_corrlibrary_restraints_ZnSqPyr本归档收录了经重精修的大分子结构，相关内容来自Kaveh H. Babai、Fei Long、Martin Malý、Keitaro Yamashita与Garib N. Murshudov合著、发表于《Acta Crystallographica Section D》的论文《Improving macromolecular structure refinement with metal coordination restraints》（利用金属配位约束优化大分子结构精修）。 描述金属配位关系的JSON文件通过MetalCoord生成，随后借助随包提供的json2restraints.py脚本将这些JSON文件转换为结构约束文件。所有大分子结构均在Servalcat中完成重精修，精修过程中采用了针对含金属配体的更新版单体字典。 所用执行命令如下： 1w9m metalCoord stats -l FS2 -o 1w9m_FS2_mc.json -p 1w9m.pdb metalCoord stats -l SF4 -o 1w9m_SF4_mc.json -p 1w9m.pdb python3 json2restraints.py -i 1w9m_*_mc.json -o 1w9m_mc_restraints -p 1w9m.pdb servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m_mc_restraints.pdb -s xray --ligand SF4_metalcoord_refined_updated.cif FS2_metalcoord_refined_updated.cif --keyword_file 1w9m_mc_restraints.txt -o 1w9m_serval_corrlibrary_restraints > 1w9m_serval_corrlibrary_restraints.log servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m.pdb -s xray --ligand SF4_metalcoord_refined_updated.cif FS2_metalcoord_refined_updated.cif -o 1w9m_serval_corrlibrary_norestraints > 1w9m_serval_corrlibrary_norestraints.log servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m.pdb -s xray -o 1w9m_serval_oldlibrary_norestraints > 1w9m_serval_oldlibrary_norestraints.log 2ynm metalCoord stats -l AF3 -o 2ynm_AF3_mc.json -p 2ynm.pdb metalCoord stats -l SF4 -o 2ynm_SF4_mc.json -p 2ynm.pdb metalCoord stats -l PMR -o 2ynm_PMR_mc.json -p 2ynm.pdb metalCoord stats -l MG -o 2ynm_MG_mc.json -p 2ynm.pdb python3 json2restraints.py -i 2ynm_*_mc.json -o 2ynm_mc_restraints -p 2ynm.pdb gemmi cif2mtz 2ynm-sf.cif 2ynm-sf.mtz servalcat refine_xtal_norefmac --adp iso --hklin 2ynm-sf.mtz --model 2ynm_mc_restraints.pdb -s xray --free 0 --ligand PMR_servalcat_updated.cif SF4_servalcat_updated.cif AF3_servalcat_updated.cif --keyword_file 2ynm_mc_restraints.txt -o 2ynm_serval_corrlibrary_restraints > 2ynm_serval_corrlibrary_restraints.log 4dl8 metalCoord stats -l AF3 -o 4dl8_AF3_mc.json -p 4dl8.pdb metalCoord stats -l MG -o 4dl8_MG_mc.json -p 4dl8.pdb metalCoord stats -l NA -o 4dl8_NA_mc.json -p 4dl8.pdb python3 json2restraints.py -i 4dl8_*_mc.json -o 4dl8_mc_restraints -p 4dl8.pdb servalcat refine_xtal_norefmac --hklin 4dl8-sf.cif --model 4dl8_mc_restraints.pdb -s xray --ligand AF3_servalcat_updated.cif --keyword_file 4dl8_mc_restraints.txt -o 4dl8_serval_coorlibrary_restraints > 4dl8_serval_coorlibrary_restraints.log 6i3j metalCoord stats -l FC6 -o 6i3j_FC6_mc.json -p 6i3j.pdb metalCoord stats -l CU -o 6i3j_CU_mc.json -p 6i3j.pdb -c 3 metalCoord stats -l NA -o 6i3j_NA_mc.json -p 6i3j.pdb python3 json2restraints.py -i 6i3j_*_mc.json -o 6i3j_mc_restraints -p 6i3j.pdb # 手动编辑6i3j_mc_restraints.pdb以删除钠原子与碳原子间的错误LINK：6i3j_mc_restraints_edit.pdb # 手动编辑6i3j_mc_restraints.txt以删除针对A620、B620号钠原子的错误约束：6i3j_mc_restraints_edit.txt # 将FC6.cif字典与TRP-HIS共价键字典手动合并：FC6_metalcoord_refined_updated_TRP-HIS.cif servalcat refine_xtal_norefmac --hklin 6i3j-sf.cif --model 6i3j_mc_restraints_edit.pdb --d_min 2.59 -s xray --ligand FC6_metalcoord_refined_updated_TRP-HIS.cif --ncsr --keyword_file 6i3j_mc_restraints_edit.txt -o 6i3j_serval_corrlibrary_restraints --vonmises > 6i3j_serval_corrlibrary_restraints.log 6wj6 metalCoord stats -l CLA -o 6wj6_CLA_mc.json -p 6wj6.cif -c 5 metalCoord stats -l HEM -o 6wj6_HEM_mc.json -p 6wj6.cif metalCoord stats -l FE2 -o 6wj6_FE2_mc.json -p 6wj6.cif python3 json2restraints.py -i 6wj6_*_mc.json -o 6wj6_mc_restraints -p 6wj6.cif # 在Coot中手动编辑6wj6_mc_restraints得到6wj6_mm01.mmcif：6wj6_mm01.mmcif servalcat refine_spa_norefmac --model 6wj6_mm01.mmcif --map emd_21690.map --source electron -d 2.58 --ncsr --ligand CLA_servalcat_updated.cif HEM_servalcat_updated.cif --keyword_file 6wj6_mc_restraints.txt -o 6wj6_mm01_serval > 6wj6_mm01_serval.log 3ayf metalCoord stats -l CA -p 3ayf.cif -o 3ayf_CA_mc.json metalCoord stats -l HEM -p 3ayf.cif -o 3ayf_HEM_mc.json metalCoord stats -l ZN -p 3ayf.cif -o 3ayf_ZN_mc.json # 采用三角双锥几何类对锌配位进行精修（普鲁斯泰因得分最低）： python3 json2restraints.py -i 3ayf_CA_mc.json 3ayf_HEM_mc.json 3ayf_ZN_mc.json -o 3ayf_restraints_mc -p 3ayf.cif servalcat refine_xtal_norefmac --hklin 3ayf-sf.cif --model 3ayf_restraints_mc.mmcif -s xray --ligand HEM.cif --keyword_file 3ayf_restraints_mc.txt -o 3ayf_serval_corrlibrary_restraints # 采用四方锥几何类对锌配位进行精修——先将3ayf_ZN_mc.json手动编辑为3ayf_ZN_mc_SqPyr.json： python3 json2restraints.py -i 3ayf_CA_mc.json 3ayf_HEM_mc.json 3ayf_ZN_mc_SqPyr.json -o 3ayf_restraints_mc_ZnSqPyr -p 3ayf.cif servalcat refine_xtal_norefmac --hklin 3ayf-sf.cif --model 3ayf_restraints_mc_ZnSqPyr.mmcif -s xray --ligand HEM.cif --keyword_file 3ayf_restraints_mc_ZnSqPyr.txt -o 3ayf_serval_corrlibrary_restraints_ZnSqPyr