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crystal structure of 23ME-00610 Fab in complex with human CD200R1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other solved structure of Fab-10F6 alone used as a serch model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Sodium Cacodylate 0.1M, Glycerol 10% (v/v), NaCl 1M, PEG 600 30.0% (w/v)
Crystal Properties Matthews coefficient Solvent content 4.32 71.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.654 α = 90 b = 98.654 β = 90 c = 279.55 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2022-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA .999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.887 93.031 94.3 0.998 16.3 25.1 27539
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.887 3.077 0.618
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.89 93.03 26177 1362 86.02 0.2036 0.2018 0.2026 0.236 0.2341 RANDOM 108.553
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.82 0.82 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.8 r_dihedral_angle_1_deg 7.171 r_mcangle_it 3.119 r_dihedral_angle_2_deg 1.955 r_mcbond_it 1.867 r_mcbond_other 1.866 r_angle_refined_deg 0.951 r_angle_other_deg 0.577 r_chiral_restr 0.045 r_bond_other_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.8 r_dihedral_angle_1_deg 7.171 r_mcangle_it 3.119 r_dihedral_angle_2_deg 1.955 r_mcbond_it 1.867 r_mcbond_other 1.866 r_angle_refined_deg 0.951 r_angle_other_deg 0.577 r_chiral_restr 0.045 r_bond_other_d 0.021 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4845 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing