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Crystal structure of H-2Kb in complex with JHMV epitope S598
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 294 0.1M cacodylate, 16% PEG 8K, 0.2M Ca(OAc)2, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.78 55.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.487 α = 90 b = 89.539 β = 111.68 c = 89.932 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
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 24.46 99.6 0.046 18 2.9 90277 90277 24.9
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 99.5 0.385 2 2.7 13114
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 1G7Q 1.8 24.4 85747 4528 99.62 0.21222 0.21023 0.2079 0.24975 0.2486 RANDOM 23.616
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] -0.66 -0.23 1.3 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.413 r_dihedral_angle_4_deg 20.931 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 9.39 r_scangle_it 4.676 r_scbond_it 3.181 r_mcangle_it 2.347 r_angle_refined_deg 1.618 r_mcbond_it 1.357 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.413 r_dihedral_angle_4_deg 20.931 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 9.39 r_scangle_it 4.676 r_scbond_it 3.181 r_mcangle_it 2.347 r_angle_refined_deg 1.618 r_mcbond_it 1.357 r_chiral_restr 0.124 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6164 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing