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The crystal structure of H-2Db with a S-glutathionylated peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1M citrate pH7.5, 28% PEG 3350, 0.2M LiSO4
Crystal Properties Matthews coefficient Solvent content 3.02 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.699 α = 90 b = 79.099 β = 90 c = 85.933 γ = 90
Symmetry Space Group P 2 2 21
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 2012-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 16 87.9 10.5 4 11701
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 15.86 10373 1176 87.9 0.21399 0.20819 0.2193 0.26668 0.2665 RANDOM 60.02
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] -1.1 4.41 -3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 19.44 r_dihedral_angle_3_deg 17.611 r_dihedral_angle_1_deg 5.528 r_scangle_it 1.502 r_angle_refined_deg 1.127 r_scbond_it 0.92 r_mcangle_it 0.574 r_mcbond_it 0.296 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 19.44 r_dihedral_angle_3_deg 17.611 r_dihedral_angle_1_deg 5.528 r_scangle_it 1.502 r_angle_refined_deg 1.127 r_scbond_it 0.92 r_mcangle_it 0.574 r_mcbond_it 0.296 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2958 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement