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Crystal Structure of the Internal UBA Domain of HHR23A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other P43 UBA-1 Y188G Structure Solved by Sulfur SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Tris pH 8.5, 1.5 M Ammonium sulfate, 12%(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 1.74 29.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.119 α = 90 b = 31.119 β = 90 c = 40.488 γ = 90
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 PILATUS 6M 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 31.12 99.71 0.0876 0.09114 0.02491 1 21.45 13.2 5180 13.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.657 100 0.8064 0.8403 0.2341 0.926 3.35 12.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE P43 UBA-1 Y188G Structure Solved by Sulfur SAD 1.6 31.12 1.39 5168 517 99.71 0.1662 0.1618 0.2054 0.1908 19.49
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 5.8786 f_angle_d 0.7048 f_chiral_restr 0.0498 f_bond_d 0.0046 f_plane_restr 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 384 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction Aimless data scaling PHASER phasing PHENIX model building Coot model building PHENIX refinement