6MC0

Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EEP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290LepnA.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.Crystals from tray 300294b8 were then soaked overnight mixed 1:1 with MCSG1(B8) condition suplemented with 5 mM ribulose-5-phosphate. Tray: 300294b8. Puck: kbr1-2
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.29α = 90
b = 67.56β = 118.82
c = 73.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2018-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1245.24799.30.0640.0740.99915.574.0662987432.21
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)RedundancyNumber Unique Reflections (All)
122.0599.60.4490.5510.7932.222.592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6EEP245.2471.3429816202099.440.15760.15420.202831.424
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 AtomsNumber
Protein Atoms3232
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms30

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction