2Y1F

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, manganese and NADPH.


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 = 67.439α = 90
b = 65.019β = 102.05
c = 86.169γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH SX-1652008-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-5MAX III911-5

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
11.964597.70.0913.6451333
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)
11.962.0788.90.41

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 2JCZ1.964548724260097.870.173930.171980.20986RANDOM19.557
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]
0.32-0.250.81-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.141
r_dihedral_angle_4_deg18.028
r_dihedral_angle_3_deg13.389
r_dihedral_angle_1_deg5.115
r_scangle_it2.459
r_scbond_it1.5
r_angle_refined_deg1.162
r_mcangle_it0.941
r_mcbond_it0.553
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.141
r_dihedral_angle_4_deg18.028
r_dihedral_angle_3_deg13.389
r_dihedral_angle_1_deg5.115
r_scangle_it2.459
r_scbond_it1.5
r_angle_refined_deg1.162
r_mcangle_it0.941
r_mcbond_it0.553
r_nbtor_refined0.292
r_symmetry_vdw_refined0.199
r_nbd_refined0.189
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.147
r_chiral_restr0.072
r_bond_refined_d0.009
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 Atoms5513
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing