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Structure of yeast pseudouridine synthase 7 (PUS7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2M Ammonium Sulfate, 10mM nickel(II) chloride, 100 mM TRIS pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.46 64.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.89 α = 90 b = 171.8 β = 90 c = 105.34 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 9M 2018-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9792 APS 21-ID-D
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 3.2 46.32 99.9 0.162 0.178 0.074 0.996 9.5 10.3 18019
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 3.2 3.42 100 1.276 1.417 0.606 0.802 2 9.7
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 5kkp 3.2 46.317 17136 881 99.88 0.2325 0.2297 0.2384 0.2869 0.2903 RANDOM 120.992
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] 0.25 -2.27 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.414 r_dihedral_angle_3_deg 17.382 r_dihedral_angle_4_deg 13.183 r_dihedral_angle_1_deg 6.868 r_angle_refined_deg 1.208 r_angle_other_deg 1.016 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.414 r_dihedral_angle_3_deg 17.382 r_dihedral_angle_4_deg 13.183 r_dihedral_angle_1_deg 6.868 r_angle_refined_deg 1.208 r_angle_other_deg 1.016 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4679 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing