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Crystal structure of broad and potent HIV-1 neutralizing antibody 438-D5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.095M sodium citrate-citric acid (pH=6.2), 16%(v/v) 2-propanol, 5% (v/v) glycerol, 17%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.93 57.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.731 α = 90 b = 97.87 β = 90 c = 125.55 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2017-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 2.06 50 99.8 0.19 0.05 0.88 22.8 11.7 71245 41.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.14 0.79 0.56 1
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 5WL2 2.06 46.37 1.34 71133 3586 99.4 0.2027 0.2005 0.2026 0.2455 0.2488 54.58
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 11.7791 f_angle_d 0.5928 f_chiral_restr 0.0457 f_plane_restr 0.0043 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6705 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement Coot model building HKL-2000 data reduction SCALEPACK data scaling PHASER phasing