2C82

X-Ray Structure Of 1-Deoxy-D-xylulose 5-phosphate Reductoisomerase, DXR, Rv2870c, From Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q0QPDB ENTRY 1Q0Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROPTHE SITTING DROPS CONTAINED 1 ML PROTEIN, 5.35 MG/ML, WITH A FINAL CONCENTRATION OF 0.64 MM OF FOSMIDOMYCIN, DISSOLVED IN 10 MM TRIS PH 8.0, AND 1 ML CRYSTALLIZATION BUFFER (40% ETHYLENE GLYCOL, 2 MM MGSO4, 20 MM DTT, 0.2 MM EDTA, AND 100 MM ACETATE PH 5.0). THE RESERVOIR SOLUTION CONSISTED OF A MIXTURE BETWEEN THE CRYSTALLIZATION BUFFER, AND THE BUFFER USED IN THE FINAL STEPS OF THE PROTEIN PURIFICATION (75 MM NACL, 10 MM TRIS-HCL PH 7.5, 20% ETHYLENE GLYCOL, 1 MM MGSO4, 10 MM DTT, 0.1 MM EDTA, AND 50 MM ACETATE PH 5.0). BEFORE THE CRYSTALS WERE FLASH-COOLED IN LIQUID NITROGEN THEY WERE TRANSFERRED TO A DROP WITH THE RESERVOIR SOLUTION COMPLEMENTED WITH AN ADDITIONAL 10% ETHYLENE GLYCOL, AND 1 MM FOSMIDOMYCIN.
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.931α = 90
b = 56.931β = 90
c = 238.997γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2005-07-17MSINGLE 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
11.94099.70.086.23.456321
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)
11.91.9599.80.39

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 1Q0Q1.94056321296299.70.2160.2150.247RANDOM35.13
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]
0.930.93-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg19.42
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg4.949
r_scangle_it3.004
r_scbond_it1.838
r_mcangle_it1.3
r_angle_refined_deg1.148
r_mcbond_it0.794
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg19.42
r_dihedral_angle_3_deg12.982
r_dihedral_angle_1_deg4.949
r_scangle_it3.004
r_scbond_it1.838
r_mcangle_it1.3
r_angle_refined_deg1.148
r_mcbond_it0.794
r_nbtor_refined0.296
r_symmetry_vdw_refined0.201
r_nbd_refined0.196
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.132
r_chiral_restr0.078
r_bond_refined_d0.009
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 Atoms334
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing