3NUE

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529520MM BTP, 150MM NACL, 0.5MM TCEP, 0.005%(V/V) THESIT, 0.2MM PEP, 0.1MM MNCL2, 0.1M NA HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.9468.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.712α = 90
b = 204.712β = 90
c = 66.264γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Double-crystal, Si(111)2005-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97929SSRLBL9-2

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
12.5501000.13410.42.85234452344
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)
12.52.591000.6332.12.852344

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 REPLACEMENTTHROUGHOUT2B7O2.538.6952324281599.980.191010.189010.22814RANDOM28.181
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.629
r_dihedral_angle_4_deg21.011
r_dihedral_angle_3_deg17.228
r_dihedral_angle_1_deg6.698
r_scangle_it4.766
r_scbond_it3.239
r_mcangle_it2.144
r_angle_refined_deg1.67
r_angle_other_deg1.305
r_mcbond_it1.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.629
r_dihedral_angle_4_deg21.011
r_dihedral_angle_3_deg17.228
r_dihedral_angle_1_deg6.698
r_scangle_it4.766
r_scbond_it3.239
r_mcangle_it2.144
r_angle_refined_deg1.67
r_angle_other_deg1.305
r_mcbond_it1.249
r_mcbond_other0.435
r_chiral_restr0.093
r_bond_refined_d0.018
r_gen_planes_refined0.014
r_gen_planes_other0.013
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6871
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms121

Software

Software
Software NamePurpose
Blu-Icedata collection
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing