DOI: 10.5281/zenodo.13694560
title: Improving macromolecular structure refinement with metal coordination restraints - examples

description: Improving macromolecular structure refinement withmetal coordination restraints - examples

This archive contains re-refined macromolecular structures presented in manuscript "Improving macromolecular structure refinement withmetal coordination restraints" written by Kaveh H. Babai, Fei Long, Keitaro Yamashita, Martin Malý and Garib N. Murshudov.

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 using Servalcat.

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

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

servalcat refine_xtal_norefmac --hklin 1w9m-sf.cif --model 1w9m.pdb -s xray -o 1w9m_serval_oldlibrary_norestraints

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

servalcat refine_xtal_norefmac --adp iso --hklin 2ynm_phases.mtz --model 2ynm_mc_restraints.pdb -s xray --ligand PMR_metalcoord_refined_updated.cif SF4_metalcoord_refined_updated.cif AF3_metalcoord_refined_updated.cif --keyword_file 2ynm_mc_restraints.txt -o 2ynm_serval_corrlibrary_restraints

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_metalcoord_refined_updated.cif --keyword_file 4dl8_mc_restraints.txt -o 4dl8_serval_coorlibrary_restraints

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

ervalcat 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

6wj6

metalCoord stats -l CLA -o 6wj6_CLA_mc.json -p 6wj6.cifmetalCoord 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 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_metalcoord_refined_updated.cif HEM_metalcoord_refined_updated.cif --keyword_file 6wj6_mc_restraints.txt -o 6wj6_mm01_serval