5E5G

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the tryptophan and phenylalanine binding sites


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M TRIS-HCL, PH 7.5, 1.5M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 10 MM D-TRYPTOPHAN
Crystal Properties
Matthews coefficientSolvent content
3.9769.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 205.002α = 90
b = 205.002β = 90
c = 66.542γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953700Australian SynchrotronMX2

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
11.9547.251000.150.0470.99814.111.2116470
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)
11.951.9899.71.4890.5330.5181.58.55694

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 3NV81.9547.25110646579899.960.16850.16770.1838RANDOM31.686
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]
-0.82-0.821.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.629
r_dihedral_angle_4_deg17.465
r_dihedral_angle_3_deg12.681
r_dihedral_angle_1_deg7.446
r_mcangle_it2.811
r_mcbond_it1.696
r_mcbond_other1.694
r_angle_refined_deg0.715
r_angle_other_deg0.571
r_chiral_restr0.036
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.629
r_dihedral_angle_4_deg17.465
r_dihedral_angle_3_deg12.681
r_dihedral_angle_1_deg7.446
r_mcangle_it2.811
r_mcbond_it1.696
r_mcbond_other1.694
r_angle_refined_deg0.715
r_angle_other_deg0.571
r_chiral_restr0.036
r_gen_planes_refined0.015
r_gen_planes_other0.006
r_bond_refined_d0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6961
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms82

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction