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- PDB-2xtj: The crystal structure of PCSK9 in complex with 1D05 Fab -

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Basic information

Entry
Database: PDB / ID: 2xtj
TitleThe crystal structure of PCSK9 in complex with 1D05 Fab
Components
  • (FAB FROM A HUMAN MONOCLONAL ANTIBODY, ...) x 4
  • (PROPROTEIN CONVERTASE ...) x 2
KeywordsHYDROLASE/ANTIBODY / HYDROLASE-ANTIBODY COMPLEX / SERINE PROTEASE / LDL-C / LDLR / EGF-A / HYPERCHOLESTEROLEMIA
Function / homology
Function and homology information


low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / low-density lipoprotein particle binding ...low-density lipoprotein particle receptor catabolic process / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / extrinsic component of external side of plasma membrane / negative regulation of sodium ion import across plasma membrane / PCSK9-LDLR complex / PCSK9-AnxA2 complex / negative regulation of receptor recycling / apolipoprotein receptor binding / very-low-density lipoprotein particle binding / low-density lipoprotein particle binding / positive regulation of low-density lipoprotein particle receptor catabolic process / LDL clearance / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of receptor internalization / COPII-coated ER to Golgi transport vesicle / endolysosome membrane / sodium channel inhibitor activity / negative regulation of low-density lipoprotein particle clearance / signaling receptor inhibitor activity / lysosomal transport / triglyceride metabolic process / low-density lipoprotein particle receptor binding / protein autoprocessing / positive regulation of receptor internalization / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / cholesterol metabolic process / regulation of neuron apoptotic process / phospholipid metabolic process / neurogenesis / VLDLR internalisation and degradation / cholesterol homeostasis / cellular response to starvation / Post-translational protein phosphorylation / kidney development / liver development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to insulin stimulus / neuron differentiation / late endosome / positive regulation of neuron apoptotic process / early endosome / lysosome / endoplasmic reticulum lumen / lysosomal membrane / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / extracellular space / RNA binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Peptidase S8 propeptide/proteinase inhibitor I9 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 ...Peptidase S8 propeptide/proteinase inhibitor I9 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDi Marco, S. / Volpari, C. / Carfi, A.
CitationJournal: J.Lipid Res. / Year: 2011
Title: A Pcsk9-Binding Antibody that Structurally Mimics the Egf(A) Domain of Ldl-Receptor Reduces Ldl Cholesterol in Vivo.
Authors: Ni, Y.G. / Di Marco, S. / Condra, J.H. / Peterson, L.B. / Wang, W. / Wang, F. / Pandit, S. / Hammond, H.A. / Rosa, R. / Cummings, R.T. / Wood, D.D. / Liu, X. / Bottomley, M.J. / Shen, X. / ...Authors: Ni, Y.G. / Di Marco, S. / Condra, J.H. / Peterson, L.B. / Wang, W. / Wang, F. / Pandit, S. / Hammond, H.A. / Rosa, R. / Cummings, R.T. / Wood, D.D. / Liu, X. / Bottomley, M.J. / Shen, X. / Cubbon, R.M. / Wang, S.P. / Johns, D.G. / Volpari, C. / Hamuro, L. / Chin, J. / Huang, L. / Zhao, J.Z. / Vitelli, S. / Haytko, P. / Wisniewski, D. / Mitnaul, L.J. / Sparrow, C.P. / Hubbard, B. / Carfi, A. / Sitlani, A.
History
DepositionOct 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
B: FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
C: FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
D: FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
E: FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05
P: PROPROTEIN CONVERTASE SUBTILISIN-KEXIN TYPE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4337
Polymers96,3936
Non-polymers401
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-60.9 kcal/mol
Surface area40980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.589, 67.834, 250.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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PROPROTEIN CONVERTASE ... , 2 types, 2 molecules AP

#1: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PROPROTEIN CONVERTASE 9 / PC9 / ...PCSK9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PROPROTEIN CONVERTASE 9 / PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9


Mass: 33083.238 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#6: Protein PROPROTEIN CONVERTASE SUBTILISIN-KEXIN TYPE 9 / PCSK9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PROPROTEIN CONVERTASE 9 / PC9 / ...PCSK9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PROPROTEIN CONVERTASE 9 / PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9


Mass: 12679.604 Da / Num. of mol.: 1 / Fragment: PRODOMAIN, RESIDUES 53-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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FAB FROM A HUMAN MONOCLONAL ANTIBODY, ... , 2 types, 2 molecules CE

#3: Protein FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05


Mass: 11588.751 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN CONSTANT DOMAIN, RESIDUES 108-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY
Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli)
#5: Protein FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05


Mass: 13113.582 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN CONSTANT DOMAIN, RESIDUES 132-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY
Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli)

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Antibody , 2 types, 2 molecules BD

#2: Antibody FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05


Mass: 11568.840 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN VARIABLE DOMAIN, RESIDUES 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY
Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli)
#4: Antibody FAB FROM A HUMAN MONOCLONAL ANTIBODY, 1D05


Mass: 14359.157 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN VARIABLE DOMAIN, RESIDUES 1-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN COMBINATORIAL ANTIBODY PHAGE DISPLAY LIBRARY
Plasmid: PMORPHX9 / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 2 types, 200 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsLEUCINE PRESENT AT A417 IN ORIGINAL CONSTRUCT. POSSIBLE NATURAL VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.34 % / Description: NONE
Crystal growMethod: vapor diffusion
Details: CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. ...Details: CRYSTALLIZATION EXPERIMENTS WERE PERFORMED AT ROOM TEMPERATURE BY THE HANGING-DROP AND SITTING-DROP METHODS. THIN PLATE-LIKE CRYSTALS WERE OBTAINED IN 100 MM NA CITRATE PH 6.5, 13% PEG 6000. FOR DATA COLLECTION CRYSTALS WERE TRANSFERRED TO A STABILIZING SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 5% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 25% PEG6000), THEN TRANSFERRED FOR 2 MIN TO A CRYOPROTECTANT SOLUTION (20 MM TRIS PH 8.0, 50 MM NACITRATE PH 6.5, 100 MM NACL, 20% GLYCEROL, 1 MM TCEP, 1 MICROM CACL2, 35% PEG6000) AND FINALLY PLACED DIRECTLY INTO LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 32238 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W2M

2w2m


Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.58 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL MODEL CONTAINS RESIDUES 61-152 FROM THE PCSK9 PRODOMAIN (CHAIN P) AND RESIDUES 155-157 AND 178-422 FROM THE PCSK9 CATALYTIC ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL MODEL CONTAINS RESIDUES 61-152 FROM THE PCSK9 PRODOMAIN (CHAIN P) AND RESIDUES 155-157 AND 178-422 FROM THE PCSK9 CATALYTIC DOMAIN (CHAIN A) THE FINAL MODEL CONTAINS RESIDUES 1-212 FROM THE FAB LIGHT CHAIN (CHAINS B AND C)AND RESIDUES 1-236 FROM THE FAB HEAVY CHAIN (CHAINS D AND E). THERE WAS NO ELECTRON DENSITY PRESENT FOR PCSK9 RESIDUES 53-60, 153-154, 158-177 AND 423-451, NOR FOR 1D05 FAB RESIDUES 237-255 OF THE CONSTANT DOMAIN OF THE HEAVY CHAIN (CHAIN E) AND RESIDUE 213 OF THE CONSTANT DOMAIN OF THE LIGHT CHAIN (CHAIN C). THESE RESIDUES WERE THEREFORE EXCLUDED FROM THE REFINEMENT. ALL OVER THE STRUCTURE, WHEN POOR DENSITY FOR SIDE CHAINS WAS PRESENT, THE CORRESPONDING RESIDUE WAS MODELED AS ALA. ALL OVER THE STRUCTURE, WHEN POOR DENSITY FOR SIDE CHAINS WAS PRESENT, THE CORRESPONDING RESIDUE WAS MODELED AS ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.25944 1629 5.1 %RANDOM
Rwork0.19992 ---
obs0.20293 30522 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---1.15 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 1 199 6075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9578178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4145780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9324.059239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36515971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3781533
X-RAY DIFFRACTIONr_chiral_restr0.1040.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22633
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24006
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.53969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05126253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32332300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3534.51924
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 136 -
Rwork0.32 2194 -
obs--99.79 %

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