3TXY

Structure of an Isochorismatase family protein (BTH_II2229) from Burkholderia thailandensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J2RPDB entry 1J2R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.2M Sodium Malonate, 0.1 M BisTris propane, 20% PEG3350, Protein 55.9 mg/ml, Cryo protection 25% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3848.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.79α = 90
b = 61.79β = 90
c = 181.77γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-09-21MSINGLE 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
11.7181.7796.70.05430.9722855-322.875
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)
11.71.7487.60.4044.48

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 REPLACEMENTTHROUGHOUTPDB entry 1J2R1.740.1122845118696.930.18180.18070.2024RANDOM15.9367
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]
0.480.240.48-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_3_deg12.37
r_dihedral_angle_4_deg11.185
r_dihedral_angle_1_deg5.546
r_angle_refined_deg1.38
r_angle_other_deg0.952
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_3_deg12.37
r_dihedral_angle_4_deg11.185
r_dihedral_angle_1_deg5.546
r_angle_refined_deg1.38
r_angle_other_deg0.952
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1407
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms4

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction