2JCY

X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthew coefficientSolvent content
2.244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.109α = 90
b = 64.817β = 101.72
c = 86.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1102006-04-06MSINGLE 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
12.3540990.0717.54.130603
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)
12.352.4193.10.19

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 2C822.354029050154099.20.1830.180.236RANDOM18.43
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]
-0.25-0.520.82-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.431
r_dihedral_angle_4_deg17.8
r_dihedral_angle_3_deg14.579
r_dihedral_angle_1_deg5.21
r_scangle_it2.034
r_scbond_it1.204
r_angle_refined_deg1.095
r_mcangle_it0.819
r_mcbond_it0.47
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.431
r_dihedral_angle_4_deg17.8
r_dihedral_angle_3_deg14.579
r_dihedral_angle_1_deg5.21
r_scangle_it2.034
r_scbond_it1.204
r_angle_refined_deg1.095
r_mcangle_it0.819
r_mcbond_it0.47
r_nbtor_refined0.29
r_symmetry_vdw_refined0.194
r_nbd_refined0.184
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.157
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_gen_planes_other
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_nbtor_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_other
r_mcbond_other
r_metal_ion_refined
r_mcangle_other
r_xyhbond_nbd_other
r_scbond_other
r_angle_other_deg
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 Atoms327
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing