5E40

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NV8PDB entry 3NV8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and 24 hours before crystal freezing, respectively
Crystal Properties
Matthews coefficientSolvent content
469.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 205.451α = 90
b = 205.451β = 90
c = 66.803γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2012-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.0519.8599.90.1430.0560.99711.87.5101083
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.091001.0260.3980.6082.17.55007

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 3NV82.0519.8596017504699.860.19480.19410.207RANDOM27.469
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]
2.442.44-4.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.373
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg12.761
r_dihedral_angle_1_deg5.242
r_mcangle_it2.339
r_mcbond_it1.279
r_mcbond_other1.279
r_angle_refined_deg1.155
r_angle_other_deg0.806
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.373
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg12.761
r_dihedral_angle_1_deg5.242
r_mcangle_it2.339
r_mcbond_it1.279
r_mcbond_other1.279
r_angle_refined_deg1.155
r_angle_other_deg0.806
r_chiral_restr0.061
r_gen_planes_refined0.009
r_bond_refined_d0.006
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7045
Nucleic Acid Atoms
Solvent Atoms537
Heterogen Atoms54

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing