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Crystal structure of bony fish MHC class I, peptide and B2m II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.35 α = 90 b = 50.65 β = 129.37 c = 90.31 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 0.97920
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 1.74 50 98.5 17.5 3.6 42201
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.79 98.3 3
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4E0R 1.74 50 40283 2140 98.53 0.17266 0.17101 0.20449 0.2122 RANDOM 32.855
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] 1.28 1.16 -6.58 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_sphericity_bonded 30.541 r_sphericity_free 23.329 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.616 r_long_range_B_refined 5.482 r_mcangle_it 4.313 r_scbond_it 4.281 r_mcbond_it 3.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_sphericity_bonded 30.541 r_sphericity_free 23.329 r_dihedral_angle_4_deg 14.829 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.616 r_long_range_B_refined 5.482 r_mcangle_it 4.313 r_scbond_it 4.281 r_mcbond_it 3.293 r_rigid_bond_restr 1.85 r_angle_refined_deg 1.048 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 3083 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement