2JD1

X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with manganese and NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C82PDB ENTRY 2C82

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.332α = 90
b = 64.888β = 101.72
c = 86.059γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2006-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12351000.1212.44.649295
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)
122.051000.48

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 2C8223546754249399.90.1770.1740.221RANDOM15.67
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]
0.2-0.040.73-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg18.725
r_dihedral_angle_3_deg13.45
r_dihedral_angle_1_deg5.18
r_scangle_it2.485
r_scbond_it1.548
r_angle_refined_deg1.166
r_mcangle_it0.941
r_mcbond_it0.507
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg18.725
r_dihedral_angle_3_deg13.45
r_dihedral_angle_1_deg5.18
r_scangle_it2.485
r_scbond_it1.548
r_angle_refined_deg1.166
r_mcangle_it0.941
r_mcbond_it0.507
r_nbtor_refined0.294
r_symmetry_vdw_refined0.198
r_nbd_refined0.194
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.135
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms5562
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing