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Crystal structure of HIV-1 broadly neutralizing antibody PGT152
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NUG PDB ENTRY 4NUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 293.15 40% PEG 600, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.99 α = 90 b = 66.3 β = 134.12 c = 84.878 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 CCD MARMOSAIC 300 mm CCD 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.8 33 99.9 0.08 28.9 7.4 42250 42208 22.8
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 4NUG 1.827 32.859 1.34 42203 2112 99.36 0.1697 0.1676 0.1692 0.2096 0.2097
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 12.058 f_angle_d 1.173 f_chiral_restr 0.081 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3413 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling