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Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2- propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1.0 M tris (base), BICINE, 40% v/v PEG 500 MME, 20% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.2 61.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.728 α = 90 b = 95.728 β = 90 c = 186.038 γ = 90
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 EIGER X 4M 2017-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97 ESRF MASSIF-3
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 2.8 47.86 99.3 0.995 9.1 7.2 41024
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 2.8 2.87 0.491
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OCC 2.8 47.86 40956 1971 99.555 0.232 0.2299 0.2644 0.247 70.396
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] 0.214 0.214 -0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.877 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_1_deg 7.554 r_lrange_it 7.215 r_lrange_other 7.215 r_scangle_it 5.041 r_scangle_other 5.04 r_mcangle_it 4.768 r_mcangle_other 4.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.877 r_dihedral_angle_4_deg 18.786 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_1_deg 7.554 r_lrange_it 7.215 r_lrange_other 7.215 r_scangle_it 5.041 r_scangle_other 5.04 r_mcangle_it 4.768 r_mcangle_other 4.768 r_scbond_it 3.187 r_scbond_other 3.187 r_mcbond_it 3.042 r_mcbond_other 3.042 r_angle_other_deg 2.427 r_angle_refined_deg 1.383 r_symmetry_xyhbond_nbd_refined 0.253 r_symmetry_nbd_refined 0.231 r_nbd_other 0.23 r_symmetry_nbd_other 0.221 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.049 r_bond_other_d 0.036 r_gen_planes_other 0.007 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8293 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing