☰ Navigation Tabs
Crystal structure of Fab in complex with MICA alpha3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XJ4 5XJ4, 4NM4, 1HYR experimental model PDB 4NM4 5XJ4, 4NM4, 1HYR experimental model PDB 1HYR 5XJ4, 4NM4, 1HYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% PEG 20000, 0.1 M Na citrate pH 5.4, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 3.31 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.778 α = 90 b = 170.432 β = 105.81 c = 148.894 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 PIXEL DECTRIS EIGER2 X 9M 2018-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.4 170.43 99.4 0.087 0.055 0.996 8.9 3.5 172438 45.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 0.734 0.478 0.653 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5XJ4, 4NM4, 1HYR 2.4 44.63 1.36 172320 8728 99.36 0.2222 0.2202 0.22 0.2595 0.2594 62.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.2494 f_angle_d 1.6024 f_chiral_restr 0.0999 f_plane_restr 0.0183 f_bond_d 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23950 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing