3HEE

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VVRPDB ENTRY 2VVR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72830.05M Tris, pH7.0, 10% PEG8000, 0.15M Magnesium chloride, 0.2M Potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
3.362.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.381α = 90
b = 69.381β = 90
c = 153.566γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C10.9999PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
125098.30.0950.09531.616.3292811.31.225.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
25098.30.0950.09531.616.329281

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VVR233.8427713148798.230.176680.174330.22051RANDOM25.078
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_dihedral_angle_4_deg18.438
r_dihedral_angle_3_deg13.511
r_dihedral_angle_1_deg6.036
r_scangle_it5.877
r_scbond_it4.113
r_mcangle_it2.241
r_angle_refined_deg2.192
r_mcbond_it1.62
r_symmetry_hbond_refined0.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_dihedral_angle_4_deg18.438
r_dihedral_angle_3_deg13.511
r_dihedral_angle_1_deg6.036
r_scangle_it5.877
r_scbond_it4.113
r_mcangle_it2.241
r_angle_refined_deg2.192
r_mcbond_it1.62
r_symmetry_hbond_refined0.435
r_nbtor_refined0.305
r_nbd_refined0.215
r_chiral_restr0.174
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.13
r_bond_refined_d0.032
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2244
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data collection
swiss-modelmodel building
REFMACrefinement
swiss-modelphasing