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Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KTD PDB entry 4KTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M Tri-lithium citrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.243 α = 92.39 b = 67.909 β = 94.13 c = 69.98 γ = 109.69
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 MAR CCD 130 mm 2013-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0000 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 1.93 69.62 95 0.045 19.2 2 62555 60025 1 1 33.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 95.8 0.549 0.549 1.1 1.9 2963
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 4KTD 1.93 36.991 1.98 62555 60010 3030 95.94 0.2343 0.2323 0.2335 0.2724 0.2732 RANDOM
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 15.413 f_angle_d 1.119 f_chiral_restr 0.073 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6578 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose JBluIce-EPICS data collection PHENIX model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing