☰ Navigation Tabs
Crystal structure of the bat MHC II molecule at 2.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 291 0.2 M Sodium phosphate dibasic dihydrate;20% w/v Polyethylene glycol 3,350;pH 9.1
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.56 α = 90 b = 92.56 β = 90 c = 108.78 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2023-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 71 99.3 0.18 0.25 5.8 18423
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 2.03 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 70.49 15041 775 93.29 0.24777 0.24565 0.2576 0.29063 0.3056 RANDOM 66.037
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] -2.83 -2.83 5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_3_deg 23.073 r_dihedral_angle_4_deg 18.153 r_long_range_B_other 13.61 r_long_range_B_refined 13.608 r_mcangle_other 9.45 r_mcangle_it 9.442 r_scangle_other 9.35 r_dihedral_angle_1_deg 8.433 r_mcbond_it 6.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.795 r_dihedral_angle_3_deg 23.073 r_dihedral_angle_4_deg 18.153 r_long_range_B_other 13.61 r_long_range_B_refined 13.608 r_mcangle_other 9.45 r_mcangle_it 9.442 r_scangle_other 9.35 r_dihedral_angle_1_deg 8.433 r_mcbond_it 6.069 r_mcbond_other 6.018 r_scbond_it 5.866 r_scbond_other 5.865 r_angle_refined_deg 1.602 r_angle_other_deg 1.196 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 3000 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing