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Crystal Structure of Ribulose-phosphate 3-epimerase from Stenotrophomonas maltophilia K279a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UMF pdb entry 5umf as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Anatrace/Calibre MCSG1 screen, condition e7: 200mM ammonium iodide, 20% (w/V) PEG 3350: StmaA.18161.a.B1.PS38644 at 18.6mg/ml, tray: 321485e7, puck: pxu9-1: cryo: 20% EG
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.89 α = 90 b = 136.48 β = 90 c = 148.74 γ = 90
Symmetry Space Group C 2 2 21
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 2021-09-16 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 1.85 50 100 0.095 0.102 0.998 17.49 7.446 72940 22.713
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 1.85 1.9 99.9 0.496 0.533 0.927 4.37 7.456
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdb entry 5umf as per Morda 1.85 40.74 1.35 72927 2050 99.96 0.1486 0.1478 0.1788 0.1708 0 19.15
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 12.3575 f_angle_d 0.8804 f_chiral_restr 0.0664 f_bond_d 0.0084 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4961 Nucleic Acid Atoms Solvent Atoms 805 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building