3R76

Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from Burkholderia lata 383 in complex with benzoate, pyruvate and glutamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R75PDB ENTRY 3R75

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12760.1 M HEPES, 0.2 M Mg-chloride, 22% isopropanol, pre-incubation on ice for 30' with 50 mM Mg-chloride, 20 mM glutamine, 20 mM chorismate, streak-seeding, pH 7.1, vapor diffusion, hanging drop, temperature 276K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4449.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 258.166α = 90
b = 97.792β = 90
c = 53.988γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDSI(111)2009-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.979SLSX10SA

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
12.629.66499.80.0617.7143071-347.384
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)
12.62.71000.3574.45

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3R752.629.6643043222799.840.16650.16330.225RANDOM52.2518
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]
-1.57-1.422.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.861
r_dihedral_angle_4_deg18.717
r_dihedral_angle_3_deg16.607
r_dihedral_angle_1_deg6.301
r_angle_other_deg2.461
r_angle_refined_deg1.572
r_chiral_restr0.083
r_bond_refined_d0.016
r_bond_other_d0.007
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.861
r_dihedral_angle_4_deg18.717
r_dihedral_angle_3_deg16.607
r_dihedral_angle_1_deg6.301
r_angle_other_deg2.461
r_angle_refined_deg1.572
r_chiral_restr0.083
r_bond_refined_d0.016
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9278
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms42

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction