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Crystal structure of HLA-G presenting KLPAQFYIL 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 16% 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 3.14 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.606 α = 90 b = 85.982 β = 95.61 c = 111.57 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 MARMOSAIC 300 mm CCD 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.7 43 0.082 33.4 119833
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 1.7 1.76 0.589 2.9 3
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 1.7 43 113595 5992 99.15 0.18382 0.18157 0.212 0.22645 0.2487 RANDOM 25.139
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] -1.38 0.57 0.67 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.364 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 12.74 r_scangle_it 7.992 r_dihedral_angle_1_deg 6.947 r_scbond_it 6.116 r_mcangle_it 3.852 r_mcbond_it 3.444 r_angle_refined_deg 1.888 r_angle_other_deg 1.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.364 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 12.74 r_scangle_it 7.992 r_dihedral_angle_1_deg 6.947 r_scbond_it 6.116 r_mcangle_it 3.852 r_mcbond_it 3.444 r_angle_refined_deg 1.888 r_angle_other_deg 1.009 r_mcbond_other 0.764 r_symmetry_vdw_other 0.331 r_xyhbond_nbd_refined 0.263 r_nbd_refined 0.249 r_nbd_other 0.231 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_refined 0.195 r_nbtor_refined 0.189 r_chiral_restr 0.128 r_nbtor_other 0.094 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6276 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing