3LS6

Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G57 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529330% PEG 5000 MME, 100mM MES Sodium Salt, 200mM Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.276α = 90
b = 77.161β = 90
c = 146.827γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC VARIMAX2009-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.542

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
11.8673.4199.30.0520.05229.25.2318113181120.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.9299.70.1920.1859.324.83140

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1G571.86503181131803161499.260.161040.161040.159190.19662RANDOM20.347
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]
0.4-0.570.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.427
r_dihedral_angle_4_deg15.378
r_dihedral_angle_3_deg13.536
r_dihedral_angle_1_deg5.369
r_scangle_it4.037
r_scbond_it2.294
r_angle_refined_deg1.322
r_mcangle_it1.298
r_mcbond_it0.696
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.427
r_dihedral_angle_4_deg15.378
r_dihedral_angle_3_deg13.536
r_dihedral_angle_1_deg5.369
r_scangle_it4.037
r_scbond_it2.294
r_angle_refined_deg1.322
r_mcangle_it1.298
r_mcbond_it0.696
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3041
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms33

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing