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.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
# 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.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
# 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.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

# 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.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

# 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.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