2D5C

Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with shikimate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WXDPDB ENTRY 1WXD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.6295Ammonium sulfate, Sodium Acetate trihydrate, PEG4000, pH 4.6, microbatch, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0138.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.811α = 90
b = 63.944β = 90
c = 113.173γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2005-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.654093.70.050.04419.32.4555535206228.3
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)
11.651.7171.60.3952.93739

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WXD1.6535.135211252062258393.50.20.20.235RANDOM34.1
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]
-7.516.141.38
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_angle_deg1.4
c_improper_angle_d0.95
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3960
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms44

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing