1YL6

crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P9LPDB ENTRY 1P9L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5292100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.957.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.13α = 90
b = 89.46β = 90
c = 77.52γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.00ELETTRA5.2R

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
12.99998.90.06123.931.11383113831-3-348.8
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)
12.92.9599.80.4944657

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1P9L2.9301255212552123798.90.204150.204150.198830.25689RANDOM59.521
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]
5.161.52-6.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.649
r_dihedral_angle_3_deg18.89
r_dihedral_angle_4_deg17.087
r_scangle_it6.644
r_dihedral_angle_1_deg6.622
r_scbond_it3.915
r_angle_refined_deg1.689
r_mcangle_it1.367
r_mcbond_it0.739
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.649
r_dihedral_angle_3_deg18.89
r_dihedral_angle_4_deg17.087
r_scangle_it6.644
r_dihedral_angle_1_deg6.622
r_scbond_it3.915
r_angle_refined_deg1.689
r_mcangle_it1.367
r_mcbond_it0.739
r_nbtor_refined0.319
r_symmetry_vdw_refined0.25
r_nbd_refined0.241
r_xyhbond_nbd_refined0.131
r_symmetry_hbond_refined0.1
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3622
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing