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Crystal structure of KD-247 Fab, an anti-V3 antibody that inhibits HIV-1 Entry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3F PDB entry 1T3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.9 294 Ammonium Sulfate, Sodium Acetate, pH 3.9, vapor diffusion, sitting drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.06 α = 90 b = 69.18 β = 90 c = 111.76 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 CCD NOIR-1 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 19.75 88.4 0.071 11 5.56 68504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.61 87.1 0.485 2.4 5.02 5995
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 1T3F 1.55 19.75 1.33 68478 2748 98.67 0.1836 0.1819 0.1682 0.2218 0.2077
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] -1.432 5.2789 -3.8468
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.573 f_angle_d 1.156 f_chiral_restr 0.067 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3342 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 62
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction d*TREK data reduction