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Crystal structure of H-2Kb in complex with the Q600Y variant of 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 6.5 294 0.1M cacodylate, 13% PEG 8K, 0.2M Ca(OAc)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.711 α = 81.11 b = 90.147 β = 70.58 c = 91.969 γ = 68.25
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++ 2007-10-29 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 2.8 27 95.8 0.101 10 2.3 44395 58.1
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 2.8 2.91 85.6 0.303 2.1 2.1 4426
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1G7Q 2.8 27 42022 2240 95.95 0.214 0.21189 0.25284 0.2479 RANDOM 41.048
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] -0.88 1.9 -2.48 -3.06 -0.95 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.217 r_dihedral_angle_3_deg 18.352 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_1_deg 5.91 r_scangle_it 1.439 r_angle_refined_deg 1.4 r_scbond_it 0.869 r_mcangle_it 0.501 r_mcbond_it 0.325 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.217 r_dihedral_angle_3_deg 18.352 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_1_deg 5.91 r_scangle_it 1.439 r_angle_refined_deg 1.4 r_scbond_it 0.869 r_mcangle_it 0.501 r_mcbond_it 0.325 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12156 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing