3T4C

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7290EBS internal tracking number 224045c2 WIZARD 3/4 C2. 24%(w/v) PEG 1500, 20%(v/v) Glycerol, BuamA.00102.a.A1 PS01117 at 74 mg/mL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.13α = 90
b = 129.5β = 90
c = 169.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.9545.9498.90.08712.716.179104-330.992
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)
11.95289.80.4012.42.8

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 DIFFRACTIONMRTHROUGHOUT3SZ81.9544.3378773395198.620.1720.170.203RANDOM28.114
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]
0.50.43-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.003
r_dihedral_angle_4_deg21.176
r_dihedral_angle_3_deg12.701
r_dihedral_angle_1_deg5.475
r_angle_refined_deg1.494
r_angle_other_deg0.969
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.003
r_dihedral_angle_4_deg21.176
r_dihedral_angle_3_deg12.701
r_dihedral_angle_1_deg5.475
r_angle_refined_deg1.494
r_angle_other_deg0.969
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7890
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction