2Y1D

X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted fosmidomycin analogue and manganese.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JD2PDB ENTRY 2JD2

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.345.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.622α = 90
b = 67.318β = 107.38
c = 84.301γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH SX-1652008-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
12.054099.50.0618.83.746664
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)
12.052.16990.43

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 2JD22.054044300235299.550.211940.209270.26146RANDOM35.305
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]
-0.81-0.920.91-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.479
r_dihedral_angle_4_deg16.273
r_dihedral_angle_3_deg14.423
r_dihedral_angle_1_deg4.871
r_scangle_it2.127
r_scbond_it1.284
r_angle_refined_deg1.05
r_mcangle_it0.911
r_mcbond_it0.513
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.479
r_dihedral_angle_4_deg16.273
r_dihedral_angle_3_deg14.423
r_dihedral_angle_1_deg4.871
r_scangle_it2.127
r_scbond_it1.284
r_angle_refined_deg1.05
r_mcangle_it0.911
r_mcbond_it0.513
r_nbtor_refined0.294
r_nbd_refined0.184
r_symmetry_vdw_refined0.153
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.114
r_chiral_restr0.065
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 Atoms5413
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing