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Crystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in complex with MPER peptide epitope.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293.15 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 30% PEG 2000 monomethyl ether, 8 MM 06:0 PA
Crystal Properties Matthews coefficient Solvent content 2.71 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.36 α = 90 b = 37.92 β = 93.68 c = 133.52 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2018-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 39.77 93.8 0.153 0.107 0.987 6.4 2.9 30972 43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 95.2 0.984 0.731 0.571 1.2 2.8
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 FREE R-VALUE 6O41 2.6 39.766 1.36 30948 1545 93.79 0.2593 0.2566 0.2605 0.31 0.3124 49
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 15.131 f_angle_d 0.536 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6821 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing