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Crystal structure of HLA-G presenting KGPPAALTL peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 18% PEG 3350, 0.2M potassium formate, 0.1M HEPES, 10mM cobalt chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.874 α = 90 b = 76.874 β = 90 c = 151.851 γ = 120
Symmetry Space Group P 32 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 MAR CCD 165 mm 2006-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 2.4 37.3 0.061 24.4 20378 38.01
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 2.4 2.49 0.416 2.8
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 1YDP 2.4 37.27 19333 1045 97.51 0.22089 0.21689 0.2588 0.29913 0.3323 RANDOM 44.309
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.675 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_4_deg 16.131 r_dihedral_angle_1_deg 6.729 r_scangle_it 5.403 r_scbond_it 4.039 r_mcangle_it 2.328 r_mcbond_it 1.915 r_angle_refined_deg 1.406 r_angle_other_deg 0.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.675 r_dihedral_angle_3_deg 16.595 r_dihedral_angle_4_deg 16.131 r_dihedral_angle_1_deg 6.729 r_scangle_it 5.403 r_scbond_it 4.039 r_mcangle_it 2.328 r_mcbond_it 1.915 r_angle_refined_deg 1.406 r_angle_other_deg 0.935 r_mcbond_other 0.341 r_symmetry_vdw_other 0.215 r_nbd_refined 0.201 r_nbd_other 0.201 r_metal_ion_refined 0.189 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.091 r_nbtor_other 0.086 r_symmetry_hbond_refined 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing