2VVP

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with its substrates ribose 5-phosphate and ribulose 5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1USLPDB ENTRY 1USL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3000, 0.1 M TRIS PH 7, 0.2 M CA ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.8356.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.832α = 90
b = 103.058β = 95.51
c = 69.728γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2005-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.653599.90.0713.33.6115358319.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7499.90.2932.9

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 1USL1.6534.71109551580599.90.1680.1660.187RANDOM13.95
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]
0.1-0.78-0.450.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.539
r_dihedral_angle_4_deg20.618
r_dihedral_angle_3_deg12.16
r_dihedral_angle_1_deg5.892
r_scangle_it2.843
r_scbond_it1.975
r_angle_refined_deg1.437
r_angle_other_deg1.311
r_mcangle_it1.05
r_mcbond_it0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.539
r_dihedral_angle_4_deg20.618
r_dihedral_angle_3_deg12.16
r_dihedral_angle_1_deg5.892
r_scangle_it2.843
r_scbond_it1.975
r_angle_refined_deg1.437
r_angle_other_deg1.311
r_mcangle_it1.05
r_mcbond_it0.993
r_symmetry_vdw_other0.343
r_nbd_refined0.215
r_nbd_other0.209
r_nbtor_refined0.172
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.125
r_symmetry_vdw_refined0.123
r_chiral_restr0.106
r_nbtor_other0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5929
Nucleic Acid Atoms
Solvent Atoms981
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing