5TJZ

Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C3V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M Sodium Chloride, 0.1 M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate
Crystal Properties
Matthews coefficientSolvent content
3.1961.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.157α = 90
b = 67.157β = 90
c = 251.325γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1APS19-ID

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
11.53095.10.05411.47.652243
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5397.80.5370.7924.3

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 REPLACEMENTTHROUGHOUT1C3V1.53049673256595.140.14860.14760.1687RANDOM29.958
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]
-0.26-0.13-0.260.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.648
r_dihedral_angle_4_deg18.114
r_dihedral_angle_3_deg11.401
r_dihedral_angle_1_deg5.483
r_scbond_it2.354
r_angle_refined_deg2.036
r_mcangle_it1.718
r_mcbond_it1.12
r_chiral_restr0.147
r_bond_refined_d0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.648
r_dihedral_angle_4_deg18.114
r_dihedral_angle_3_deg11.401
r_dihedral_angle_1_deg5.483
r_scbond_it2.354
r_angle_refined_deg2.036
r_mcangle_it1.718
r_mcbond_it1.12
r_chiral_restr0.147
r_bond_refined_d0.019
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1807
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing