3TMQ

Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei in complex with D-arabinose-5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SZ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Internal tracking number224822. PACT screen F5. 0.2M Sodium nitrate, 0.1M BIS-TRIS propane, 20% PEG3350, protein drop contains 10mM D-arabinose-5-phosphate. BupsA.00102a.A1 PS00621 30.3mg/ml., pH 6.5, vapor diffusion, sitting drop, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.72α = 90
b = 92.08β = 90
c = 152.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.0549.2980.10613.875.328021978647-326.74
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)
12.052.187.70.5533.14.31

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 REPLACEMENTTHROUGHOUT3SZ82.149.273746367998.840.1810.1790.217RANDOM20.633
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]
-0.742.19-1.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.557
r_dihedral_angle_4_deg18.216
r_dihedral_angle_3_deg11.906
r_dihedral_angle_1_deg5.918
r_angle_refined_deg1.415
r_angle_other_deg1.122
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.557
r_dihedral_angle_4_deg18.216
r_dihedral_angle_3_deg11.906
r_dihedral_angle_1_deg5.918
r_angle_refined_deg1.415
r_angle_other_deg1.122
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8044
Nucleic Acid Atoms
Solvent Atoms629
Heterogen Atoms88

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MD2data collection
XDSdata reduction