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Crystal structure of UMPK from S. aureus in complex with U5P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 2.0 M Sodium formate, 0.1 M Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.357 α = 90 b = 96.302 β = 103.452 c = 75.84 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 200K 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.26 13.033166057 97.9 0.15 0.981 5.7 4.2 12652 72.5030204684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.26 3.38 0.754 0.662
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.2600733561 13.033166057 1.34352298322 12621 594 99.1905061301 0.238000242382 0.235991176995 0.2367 0.276253695761 0.2769 86.8245662998
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 16.0979857195 f_angle_d 0.616318408869 f_chiral_restr 0.0443666477659 f_bond_d 0.00385458692454 f_plane_restr 0.00329802084498
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5379 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 21
Software Software Software Name Purpose CrysalisPro data reduction PHENIX refinement PHASER phasing Aimless data scaling