2Y1E

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JCZPDB ENTRY 2JCZ

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.487α = 90
b = 64.754β = 101.97
c = 86.005γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2008-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.654496.50.0713.73.884235
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)
11.651.7480.10.39

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 2JCZ1.654479964425196.420.187040.185650.21269RANDOM16.726
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]
-0.03-0.260.68-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.035
r_dihedral_angle_4_deg15.78
r_dihedral_angle_3_deg11.921
r_dihedral_angle_1_deg4.632
r_scangle_it2.267
r_scbond_it1.356
r_angle_refined_deg1.006
r_mcangle_it0.864
r_mcbond_it0.501
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.035
r_dihedral_angle_4_deg15.78
r_dihedral_angle_3_deg11.921
r_dihedral_angle_1_deg4.632
r_scangle_it2.267
r_scbond_it1.356
r_angle_refined_deg1.006
r_mcangle_it0.864
r_mcbond_it0.501
r_nbtor_refined0.295
r_symmetry_vdw_refined0.194
r_nbd_refined0.189
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.109
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms5509
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing