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CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX THE WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P,Y4A)
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 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.84 α = 90 b = 125.12 β = 128.15 c = 101.32 γ = 90
Symmetry Space Group C 1 2 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 2008-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 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 2.49 49.21 99.9 0.152 10 3.9 40587 40587 55
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 2.61 99.9 0.83 2.1 3.9 5927
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 2.49 49.21 38455 38455 2006 99.62 0.23164 0.23164 0.22961 0.2334 0.27044 0.2648 RANDOM 52.417
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] 0.47 0.37 -0.1 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.408 r_dihedral_angle_4_deg 21.445 r_dihedral_angle_3_deg 19.157 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.622 r_angle_refined_deg 1.341 r_scbond_it 1.036 r_angle_other_deg 0.958 r_mcangle_it 0.601 r_mcbond_it 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.408 r_dihedral_angle_4_deg 21.445 r_dihedral_angle_3_deg 19.157 r_dihedral_angle_1_deg 6.406 r_scangle_it 1.622 r_angle_refined_deg 1.341 r_scbond_it 1.036 r_angle_other_deg 0.958 r_mcangle_it 0.601 r_mcbond_it 0.318 r_mcbond_other 0.093 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 6220 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 22
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling