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Crystal structure of the unbound Fab fragment of the human HIV-1 neutralizing antibody PGZL1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 Reservoir: 20% PEG 4000, 20% glycerol, 0.08 M sodium acetate pH 4.6, 0.16 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.54 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.59 α = 90 b = 96.021 β = 120.18 c = 67.325 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 NULL 2017-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) 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 1.4 37.0477 95.4 0.082 0.052 7.8 3.3 89730 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 83.2 0.891 0.609 1.4 2.7
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 2fx7 1.402 37.035 1.34 89715 4486 95.33 0.1481 0.1464 0.1494 0.1812 0.1829 24
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 20.742 f_angle_d 1.391 f_chiral_restr 0.116 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3288 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing