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Crystal Structure of the Murine MHC Class Ib Molecule M10.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K8D PDB ENTRY 1K8D (confirmed with 3FRU) experimental model PDB 3FRU PDB ENTRY 1K8D (confirmed with 3FRU)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1 M imidazole, 20% PEG 1000, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.11 α = 90 b = 134.71 β = 90 c = 149.37 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 double crystal monochromator 2005-04-03 M SINGLE WAVELENGTH 2 1 100 CCD ADSC QUANTUM 315 double crystal monochromator 2005-04-27
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.11587 ALS 12.3.1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 1.00879 SSRL BL9-2
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 3 99 91.2 0.156 0.156 9 5.7 46977 46977 76.6
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 3 3.11 64.8 64.8 0.535 0.535 2.7 2.7 3287
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 1K8D (confirmed with 3FRU) 3 56.36 46898 46898 2355 92.3 0.307 0.307 0.307 0.2938 0.308 0.2997 Thin shell method 59.1
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] 0.3 -3.09 2.79
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_angle_deg 1.6 c_improper_angle_d 0.83 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13665 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement PDB_EXTRACT data extraction