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Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 LepnA.00944.a.B1.PS38423 at 22.85 mg/ml was mixed 1:1 with MCSG1(B8): 25.5% (w/v) PEG-4,000, 15% (v/v) Glycerol, 0.085 M Tris Base / Hydrochloric, 0.17 M Sodium Acetate, pH = 8.5. Tray: 300294b8. Puck: jve-8
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.63 α = 90 b = 67.93 β = 119.54 c = 74 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2018-06-28 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 32.19 97.7 0.058 0.067 0.998 13.97 4.117 37853 33.33
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 97.3 0.548 0.626 0.813 2.54 4.242
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 FREE R-VALUE 4X84 1.85 32.19 36108 2210 93.5 0.1613 0.1578 0.1592 0.2164 0.2171 random 30.0075
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3219 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing