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Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-2*040202 For 2.3 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M sodium acetate pH4.6
25% polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.802 α = 90 b = 101.802 β = 90 c = 73.455 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.0
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 2.31 88.16 89.9 0.01538 22.96 11.1 19686
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 2.31 2.5 0.099
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5H94 2.31 88.16 16579 896 88.53 0.2029 0.19905 0.2047 0.27605 0.2781 RANDOM 40.541
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] -0.29 -0.15 -0.29 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.479 r_dihedral_angle_3_deg 17.62 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_1_deg 8.94 r_long_range_B_refined 4.92 r_long_range_B_other 4.861 r_angle_refined_deg 2.033 r_mcangle_other 1.977 r_mcangle_it 1.975 r_scangle_other 1.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.479 r_dihedral_angle_3_deg 17.62 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_1_deg 8.94 r_long_range_B_refined 4.92 r_long_range_B_other 4.861 r_angle_refined_deg 2.033 r_mcangle_other 1.977 r_mcangle_it 1.975 r_scangle_other 1.727 r_angle_other_deg 1.147 r_mcbond_it 1.12 r_mcbond_other 1.111 r_scbond_it 0.984 r_scbond_other 0.984 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing