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Crystal structure of BAK L100A in complex with activating antibody fragments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 38.9 % 2-methyl-2,4-pentanediol,
0.1 M Sodium cacodylate pH 6.44,
4 % Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 3.23 61.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.17 α = 90 b = 271.8 β = 91.79 c = 74.04 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 100 PIXEL DECTRIS EIGER2 X 9M 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 3.1 39.385 98.5 0.98 6.8 3.5 40131 66.95
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 3.1 3.21 98.1 0.43 1.2
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 5W5X 3.1 39.385 1.34 40131 1711 98.46 0.2164 0.2144 0.217 0.2621 0.2648 85.1927
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 16.022 f_angle_d 0.502 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11533 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction XDS data scaling