3UND

Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TMQPDB ENTRY 3tmq

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290EBS internal tracking number 227318B6, from a focus screen based on PACT F12. 0.2 M malonate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, 10 mM D-arabinose-5-phosphate, 10 mM phosphoenolpyruvate, vapor diffusion, sitting drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3251.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.84α = 90
b = 146.24β = 90
c = 178.94γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.541780

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
12.15097.30.0819.545.671084-327.104
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)
12.12.1594.20.3764.44.8

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 DIFFRACTIONMRTHROUGHOUTPDB ENTRY 3tmq2.15071015358197.340.1680.1670.192RANDOM24.112
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]
0.77-1.791.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.598
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg6.072
r_angle_refined_deg1.593
r_angle_other_deg1.233
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.598
r_dihedral_angle_4_deg18.461
r_dihedral_angle_3_deg12.189
r_dihedral_angle_1_deg6.072
r_angle_refined_deg1.593
r_angle_other_deg1.233
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8444
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms204

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction