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Crystal structure of H-2Db in complex with JHMV epitope S510
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BZ9 PDB entry 1BZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 0.1M sodium citrate, 28% PEG 3350, 0.2M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.87 57.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.538 α = 90 b = 86.056 β = 90.01 c = 152.072 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 ADSC QUANTUM 210 2006-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 58.4 95.4 0.056 0.056 8.2 2.8 113937 113937 30.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 97.3 0.185 0.185 4.8 2.7 16934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1BZ9 2.1 56.98 108198 108198 5737 95.05 0.20936 0.20936 0.20635 0.2022 0.26614 0.2595 RANDOM 27.903
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] 1.2 0.13 -1.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_4_deg 17.511 r_dihedral_angle_3_deg 16.038 r_dihedral_angle_1_deg 7.175 r_scangle_it 5.21 r_scbond_it 3.672 r_mcangle_it 2.66 r_mcbond_it 1.791 r_angle_refined_deg 1.741 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_4_deg 17.511 r_dihedral_angle_3_deg 16.038 r_dihedral_angle_1_deg 7.175 r_scangle_it 5.21 r_scbond_it 3.672 r_mcangle_it 2.66 r_mcbond_it 1.791 r_angle_refined_deg 1.741 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12061 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing