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Crystal structure of UMPK from S. aureus in complex with ATP and GTP
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 0.7 M Ammonium tartrate dibasic, 0.1 M Tris pH 8.5, 0.1 M Adenosine-5'-triphosphate disodium salt hydrate
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.788 α = 90 b = 194.788 β = 90 c = 118.746 γ = 120
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 16M 2022-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97902 SSRF BL10U2
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 2.88 48.7 100 0.15 0.998 11.8 7.3 114053 56.743492024
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 2.88 2.93 0.877 0.854
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 2.88001234592 48.697 1.96332996786 113829 5652 99.8114762723 0.205557077968 0.202893139248 0.2034 0.257805710856 0.2566 66.8108872011
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 17.1475153293 f_angle_d 0.595292215894 f_chiral_restr 0.0435919386838 f_plane_restr 0.00303431628056 f_bond_d 0.00297199011024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32406 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 586
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling PHASER phasing