4E4T

Crystal structure of Phosphoribosylaminoimidazole carboxylase, ATPase subunit from Burkholderia ambifaria


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q2O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289BuamA.00036.a.A1 PS01234 at 46 mg/mL against Wiz3/4 condition H5, 20% PEG 8000, 0.1 M Hepes pH 7.5, 0.2 M ammonium sulfate, 10% isopropanol with 20% ethylene glycol as cryo-protectant, crystal tracking ID 228074h5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1843.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.43α = 90
b = 73.39β = 90
c = 159.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
11.555099.60.05415.764.5111915111431-324.671
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)
11.551.5999.40.4732.74

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 REPLACEMENTTHROUGHOUT3q2o1.5550111430558699.560.17850.17720.2028RANDOM22.5074
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]
-0.960.090.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.498
r_dihedral_angle_4_deg13.067
r_dihedral_angle_3_deg10.752
r_dihedral_angle_1_deg5.45
r_angle_refined_deg1.427
r_angle_other_deg1.11
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.498
r_dihedral_angle_4_deg13.067
r_dihedral_angle_3_deg10.752
r_dihedral_angle_1_deg5.45
r_angle_refined_deg1.427
r_angle_other_deg1.11
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5612
Nucleic Acid Atoms
Solvent Atoms801
Heterogen Atoms25

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction