3V7N

Crystal structure of Threonine synthase (thrC) from from Burkholderia thailandensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KL7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5290EBS internal tracking number 225991F9: Wizard3/4 F9. 25% PEG 1500, 0.1 M MIB buffer/HCl pH 5.0. ButhA.00545.a.A1 PW33400 at 44.8 mg/mL, vapor diffusion, sitting drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.56α = 90
b = 90.24β = 90
c = 98.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033180APS23-ID-B

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
11.45099.30.06414.744.8497539-318.564
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)
11.41.4499.70.5672.84.78

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 REPLACEMENTTHROUGHOUT1KL71.45097538487199.350.1610.160.181RANDOM15.198
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]
-0.490.140.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.786
r_dihedral_angle_4_deg13.269
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg5.671
r_angle_refined_deg1.767
r_angle_other_deg0.996
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.786
r_dihedral_angle_4_deg13.269
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg5.671
r_angle_refined_deg1.767
r_angle_other_deg0.996
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3546
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms35

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction