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Murine class I major histocompatibility complex H-2Kb in complex with post-translationally modified LCMV-derived gp34-41 peptide, comprising a nitrotyrosine at position 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7Q PDB ENTRY 1S7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.7 293 1.8 M NaH2PO4/K2HPO4, 1.5% MPD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.466 α = 90 b = 88.496 β = 94.71 c = 119.05 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 315r 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.6 50.3 100 0.119 0.119 12.9 4.3 32268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.75 100 0.39 3.3 4.3
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 (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 1S7Q 2.6 50.3 30630 30630 1654 100 0.249 0.246 0.2497 0.295 0.2975 RANDOM 31.2
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] 0.03 -0.08 -0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 19.251 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 7.778 r_scangle_it 2.6 r_scbond_it 1.5 r_angle_refined_deg 1.285 r_mcangle_it 1.102 r_angle_other_deg 0.826 r_mcbond_it 0.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.215 r_dihedral_angle_4_deg 19.251 r_dihedral_angle_3_deg 15.588 r_dihedral_angle_1_deg 7.778 r_scangle_it 2.6 r_scbond_it 1.5 r_angle_refined_deg 1.285 r_mcangle_it 1.102 r_angle_other_deg 0.826 r_mcbond_it 0.573 r_mcbond_other 0.101 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6176 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 24
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling