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Crystal structure of a HLA-B*35:01-HPVG-D5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FYY pdb entry 2FYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 16% PEG 4000, 0.2M ammonium acetate and 0.1M Na-Citrate pH 5.6, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.64 α = 90 b = 81.23 β = 90 c = 109.1 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 CCD ADSC-Q210 2012-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.984 Australian Synchrotron MX1
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 1.8 50 100 0.066 26.2 42487 42487 -3 16.61
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 1.8 1.9 100 0.447 4.76
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 2FYY 1.8 45.286 1.34 42480 42480 2112 99.95 0.1806 0.1789 0.1749 0.2132 0.2087 randomn 20.59
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] -2.2434 -3.3529 5.5963
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.747 f_angle_d 1.097 f_chiral_restr 0.082 f_bond_d 0.01 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3177 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection