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Crystal structure of DUCK MHC CLASS I for 1.71 angstrom
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 277 8% w/v Polyethylene glycol 1000, 8% w/v Polyethylene glycol 8000, 20% v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.27 α = 90 b = 64.39 β = 105.74 c = 77.92 γ = 90
Symmetry Space Group P 1 21 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++ 2013-05-16 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) 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 1.71 50 96.2 0.063 0.063 20.759 4.5 41752
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 1.8 1.86 98.2 0.542 2.667 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4E0R 1.71 50 40154 2100 89.5 0.15878 0.1568 0.1515 0.19739 0.1916 RANDOM 33.273
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] 0.04 -0.81 0.23 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_sphericity_free 32.179 r_sphericity_bonded 25.712 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 15.588 r_rigid_bond_restr 11.618 r_long_range_B_refined 9.559 r_scbond_it 9.125 r_mcangle_it 7.193 r_dihedral_angle_1_deg 6.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_sphericity_free 32.179 r_sphericity_bonded 25.712 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 15.588 r_rigid_bond_restr 11.618 r_long_range_B_refined 9.559 r_scbond_it 9.125 r_mcangle_it 7.193 r_dihedral_angle_1_deg 6.65 r_mcbond_it 6.332 r_angle_refined_deg 1.931 r_chiral_restr 0.157 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 3034 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement