3HE8

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72830.05M Tris, pH7.0, 10% PEG8000, 0.15M Magnesium chloride, 0.2M Potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
3.3363.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.515α = 90
b = 69.515β = 90
c = 154.434γ = 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
11.95092.20.0350.05163.121.1322281.71.325.9
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)
11.95092.20.0510.05163.121.132228

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 2VVR1.928.811.31.73222830510163092.150.189240.187630.22011RANDOM25.936
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.262
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg12.696
r_dihedral_angle_1_deg5.298
r_scangle_it3.769
r_scbond_it2.525
r_mcangle_it1.378
r_angle_refined_deg1.332
r_mcbond_it0.875
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.262
r_dihedral_angle_4_deg18.707
r_dihedral_angle_3_deg12.696
r_dihedral_angle_1_deg5.298
r_scangle_it3.769
r_scbond_it2.525
r_mcangle_it1.378
r_angle_refined_deg1.332
r_mcbond_it0.875
r_nbtor_refined0.301
r_nbd_refined0.203
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.124
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2244
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms12

Software

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