5TJY

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29850 mM Ammonium Sulfate, 50 mM Bis-Tris pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH)
Crystal Properties
Matthews coefficientSolvent content
3.0960.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.421α = 90
b = 66.421β = 90
c = 249.363γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-10MSINGLE 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)Rrim I (All)Rpim I (All)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
12.44099.90.1020.1050.0237.320.513744
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)
12.42.441000.8130.94720.7

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 REPLACEMENTTHROUGHOUT1C3V2.4401291466399.520.1480.14560.1949RANDOM43.662
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]
0.990.50.99-3.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.123
r_dihedral_angle_4_deg20.04
r_dihedral_angle_3_deg12.363
r_dihedral_angle_1_deg6.331
r_mcangle_it4.312
r_mcbond_other3.211
r_mcbond_it3.209
r_angle_refined_deg1.914
r_angle_other_deg1.012
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.123
r_dihedral_angle_4_deg20.04
r_dihedral_angle_3_deg12.363
r_dihedral_angle_1_deg6.331
r_mcangle_it4.312
r_mcbond_other3.211
r_mcbond_it3.209
r_angle_refined_deg1.914
r_angle_other_deg1.012
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1807
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms108

Software

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