5TEK

Apo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YL5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.569α = 90
b = 122.607β = 90
c = 80.846γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
124099.60.0610.061135.540777-3
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)
122.0399.30.6550.8564.8

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 REPLACEMENTTHROUGHOUT1YL52.014038724202398.970.19320.1920.2167RANDOM55.381
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]
3.68-1.4-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.279
r_dihedral_angle_4_deg23.114
r_dihedral_angle_3_deg12.898
r_dihedral_angle_1_deg5.561
r_angle_other_deg3.745
r_mcangle_it2.802
r_mcbond_it1.811
r_mcbond_other1.81
r_angle_refined_deg1.558
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.279
r_dihedral_angle_4_deg23.114
r_dihedral_angle_3_deg12.898
r_dihedral_angle_1_deg5.561
r_angle_other_deg3.745
r_mcangle_it2.802
r_mcbond_it1.811
r_mcbond_other1.81
r_angle_refined_deg1.558
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3639
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing