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Crystal structure of feline MHC class I for 2,1 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG/Ion solution No. 23 (0.2M ammonium formate and 20%(w/v) polyethylene glycol 3,350)
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.421 α = 90 b = 83.379 β = 90 c = 121.636 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.1 50 99.55 0.542 0.063 7.31 12.7 27016
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 2.103 2.157 99.55 0.542 0.063 30.971 4.5
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 3PWV 2.1 50 27016 1404 98.55 0.21533 0.2133 0.2114 0.25521 0.2568 RANDOM 35.479
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] -3.24 0.53 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_sphericity_free 27.6 r_dihedral_angle_4_deg 13.682 r_dihedral_angle_3_deg 13.448 r_sphericity_bonded 11.659 r_dihedral_angle_1_deg 5.296 r_long_range_B_refined 2.841 r_scbond_it 1.728 r_mcangle_it 1.634 r_mcbond_it 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.479 r_sphericity_free 27.6 r_dihedral_angle_4_deg 13.682 r_dihedral_angle_3_deg 13.448 r_sphericity_bonded 11.659 r_dihedral_angle_1_deg 5.296 r_long_range_B_refined 2.841 r_scbond_it 1.728 r_mcangle_it 1.634 r_mcbond_it 1.33 r_rigid_bond_restr 1.044 r_angle_refined_deg 0.919 r_chiral_restr 0.067 r_bond_refined_d 0.005 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 3135 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing