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Structure of anti-C3d Fab(3d8b) in complex with C3d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ONT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 15% PEG 10,000, 0.1 M bicine pH 7.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.372 α = 90 b = 62.229 β = 108.03 c = 85.547 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 6M 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
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 1.75 49.47 99.5 0.998 15.23 3.71 73836
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 1.75 1.86 0.699
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 (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 4ONT 1.75 49.47 70146 3673 99.5 0.1725 0.171 0.1827 0.2014 0.2059 RANDOM 21.725
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] 0.62 -0.22 -0.12 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.848 r_angle_other_deg 1.49 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.848 r_angle_other_deg 1.49 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5741 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing