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HLA-A24 in complex with HIV-1 Nef134-8(wt)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 3350, 200 mM sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.687 α = 90 b = 67.07 β = 99.01 c = 117.727 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2011-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 97.7 17.4 5 35040
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3VXN 2.4 50 32496 1713 97.74 0.2333 0.2314 0.2303 0.2709 0.2688 RANDOM 34.421
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] -0.56 -1.18 0.36 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.969 r_dihedral_angle_4_deg 22.176 r_dihedral_angle_3_deg 18.05 r_dihedral_angle_1_deg 5.302 r_angle_refined_deg 0.925 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6252 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms
Software Software Software Name Purpose SCALA data reduction MOLREP model building REFMAC refinement PDB_EXTRACT data extraction