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Fab 3B6 bound to ApoL1 NTD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 40% MPD, 5% PEG 8000, 0.1M Na Cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.72 66.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.753 α = 80.16 b = 71.867 β = 85.05 c = 123.436 γ = 90.16
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 300K 2016-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.857 70.99 89.6 0.059 0.059 0.998 3.6 3.2 82724
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 1.858 2.044 52.2 0.574 0.701 0.496 0.635 1.6 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 THROUGHOUT 2VL5 1.857 70.799 1.96 82636 4035 55.02 0.2065 0.2047 0.2117 0.2416 0.2435 55.7817
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 13.648 f_angle_d 1.31 f_chiral_restr 0.048 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7841 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing