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CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P, Y4F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.12 60.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.82 α = 90 b = 124.27 β = 103.29 c = 99.65 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 4 2008-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93400 ESRF ID14-2
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 2.5 48.5 98.1 0.112 10.7 3.7 75693 75693 55.1
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 2.5 2.65 99.2 0.631 1.9 11100
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 1S7U 2.5 20 70600 70600 3749 97.9 0.28604 0.28604 0.28449 0.2844 0.31473 0.3143 RANDOM 38.631
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] -0.12 -0.87 0.1 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 23.293 r_dihedral_angle_3_deg 17.503 r_dihedral_angle_1_deg 6.345 r_scangle_it 1.254 r_angle_refined_deg 1.192 r_angle_other_deg 0.817 r_scbond_it 0.814 r_mcangle_it 0.482 r_mcbond_it 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 23.293 r_dihedral_angle_3_deg 17.503 r_dihedral_angle_1_deg 6.345 r_scangle_it 1.254 r_angle_refined_deg 1.192 r_angle_other_deg 0.817 r_scbond_it 0.814 r_mcangle_it 0.482 r_mcbond_it 0.262 r_mcbond_other 0.076 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 12264 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling