2VVQ

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
115% PEG 8000,0.1 M MES PH6, 5% PEG 1000, 0.2 M LISO4
Crystal Properties
Matthews coefficientSolvent content
2.7955.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.369α = 90
b = 102.119β = 96.18
c = 69.604γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2005-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
1281.6598.50.099.72.662962317
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)
122.1197.70.3932.6

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 1USL25059767319398.30.1610.1590.193RANDOM12.1
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]
-0.48-0.37-0.010.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.579
r_dihedral_angle_4_deg19.353
r_dihedral_angle_3_deg12.943
r_dihedral_angle_1_deg6.334
r_scangle_it2.27
r_mcangle_it2.077
r_mcbond_it1.458
r_scbond_it1.454
r_angle_refined_deg1.408
r_angle_other_deg1.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.579
r_dihedral_angle_4_deg19.353
r_dihedral_angle_3_deg12.943
r_dihedral_angle_1_deg6.334
r_scangle_it2.27
r_mcangle_it2.077
r_mcbond_it1.458
r_scbond_it1.454
r_angle_refined_deg1.408
r_angle_other_deg1.008
r_symmetry_vdw_other0.327
r_nbd_refined0.237
r_nbd_other0.202
r_nbtor_refined0.169
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.138
r_symmetry_vdw_refined0.131
r_nbtor_other0.085
r_chiral_restr0.082
r_bond_refined_d0.013
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 Atoms5915
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing