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MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAA PDB ENTRY 2VAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 2.3M Na/K PHOSPHATE, 2% MPD, pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.87 α = 90 b = 86.84 β = 90 c = 44.98 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 133 IMAGE PLATE MARRESEARCH DOUBLE-FOCUSING MIRRORS 1996-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 20 89.3 0.078 16.2 5.4 28511 34.8
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 2.1 2.17 55 0.384 1.9 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT PDB ENTRY 2VAA 2.2 18 26120 2605 94 0.224 0.224 0.279 RANDOM 30.8
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.2 x_scangle_it 4.96 x_scbond_it 3.43 x_mcangle_it 3.32 x_mcbond_it 2.11 x_angle_deg 1.4 x_improper_angle_d 1.3 x_bond_d 0.008 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.2 x_scangle_it 4.96 x_scbond_it 3.43 x_mcangle_it 3.32 x_mcbond_it 2.11 x_angle_deg 1.4 x_improper_angle_d 1.3 x_bond_d 0.008 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3121 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building X-PLOR refinement X-PLOR phasing