3IXR

Crystal Structure of Xylella fastidiosa PrxQ C47S Mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Crystallized in presence of 10 mM DTT. The optimal condition was obtained with the reservoir solution comprising 0.1 M Hepes-NaOH (pH 7.5) and 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.973α = 90
b = 39.743β = 90
c = 99.836γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCDmirrors2008-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.549LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.630.798.010.0636.313.3208321969726.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6495.460.366.113.4

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 1E2Y1.627.8319695106598.020.198360.195790.24669RANDOM20.433
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]
-0.190.38-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.548
r_dihedral_angle_3_deg13.787
r_dihedral_angle_4_deg11.404
r_dihedral_angle_1_deg7.065
r_scangle_it5.313
r_scbond_it3.616
r_mcangle_it2.445
r_angle_refined_deg2.354
r_mcbond_it1.512
r_chiral_restr0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.548
r_dihedral_angle_3_deg13.787
r_dihedral_angle_4_deg11.404
r_dihedral_angle_1_deg7.065
r_scangle_it5.313
r_scbond_it3.616
r_mcangle_it2.445
r_angle_refined_deg2.354
r_mcbond_it1.512
r_chiral_restr0.182
r_bond_refined_d0.028
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1244
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling