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Crystal structure of Swine MHC CLASSI for 1.48 angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 20%(w/v) Polyethylene glycol 3350, 0.2M Ammonium fluoride
Crystal Properties Matthews coefficient Solvent content 2.3 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.453 α = 90 b = 41.471 β = 117.46 c = 106.735 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 315 2014-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 0.97892
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 50 99.8 19.482 3.7 127299
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 1.48 1.518 99.8 0.384 3.536 3.6
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 3QQ4 1.48 50 127299 6668 99.61 0.15177 0.14975 0.1465 0.19025 0.1896 RANDOM 21.929
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] 0.5 1.28 -4.47 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_sphericity_free 28.64 r_sphericity_bonded 24.733 r_dihedral_angle_4_deg 20.394 r_dihedral_angle_3_deg 13.035 r_rigid_bond_restr 8.273 r_dihedral_angle_1_deg 6.353 r_long_range_B_refined 5.171 r_scbond_it 5.107 r_mcangle_it 3.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_sphericity_free 28.64 r_sphericity_bonded 24.733 r_dihedral_angle_4_deg 20.394 r_dihedral_angle_3_deg 13.035 r_rigid_bond_restr 8.273 r_dihedral_angle_1_deg 6.353 r_long_range_B_refined 5.171 r_scbond_it 5.107 r_mcangle_it 3.96 r_mcbond_it 3.264 r_angle_refined_deg 2.171 r_chiral_restr 0.17 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6220 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data reduction PHASER data scaling PHENIX phasing