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Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MDX PDB entry 3mdx as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 RigakuReagents JCSG+ screen, condition H7: 25% (w/V) PEG 3350, 100mM BisTris / HCl pH 6.5, 200mM ammonium sulfate: RiprA.10050.a.A1.PW00480 at 48mg/ml: tray 320497 h7: cryo: 15% EG: puck: lrw3-2
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.37 α = 90 b = 97.39 β = 118.597 c = 100.54 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 CCD RAYONIX MX-300 Beryllium Lenses 2021-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.15 50 98.7 0.045 0.053 0.999 18.57 3.629 91387 35.916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 91.6 0.215 0.27 0.952 4.31 2.607
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3mdx as per MoRDa 2.15 48.69 1.37 91323 1866 98.84 0.1595 0.1587 0.159 0.2006 0.1999 0 32.86
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 12.2088 f_angle_d 0.8468 f_chiral_restr 0.062 f_bond_d 0.0068 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12059 Nucleic Acid Atoms Solvent Atoms 1111 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing Coot model building