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Crystal structure of a multiple lysine-to-arginine substitution mutant of the human CRIg C3b-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ICC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M sodium acetate (pH 6.5)
0.2 M ammonium acetate
30% (w/v) PEG-4000
Crystal Properties Matthews coefficient Solvent content 1.75 29.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.826 α = 90 b = 50.28 β = 90 c = 60.975 γ = 90
Symmetry Space Group P 21 21 21
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 2020-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.25 50 94 0.107 0.114 0.039 0.986 20.3 7.8 25835
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.29 90.5 0.349 0.373 0.129 0.946 7.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.251 30.487 25744 1997 92.84 0.1661 0.1636 0.1649 0.1958 0.197
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.152 f_angle_d 0.792 f_chiral_restr 0.088 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 962 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing