4QGR

Crystal structure of a DegT DnrJ EryC1 StrS aminotransferase from Brucella abortus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NU7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289BrabA.17333.a.B1.PS02033 at 20 mg/mL against MCSG-1 screen condition F2 0.2 M ammonium acetate, 0.1 M BisTris HCl pH 6.5, 25% PEG 3350 supplemented with 25% ethylene glycol as cryo-protectant, crystal tracking ID 254589f2, unique puck ID xrf9-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2645.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.69α = 90
b = 92.06β = 96.82
c = 86.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.12709SSRLBL7-1

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
11.755099.50.07213.613.77470374295-325.269
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)
11.751.8990.5472.32

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 REPLACEMENTTHROUGHOUT3NU71.755074272368899.470.15740.15590.1851RANDOM24.456
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]
0.020.03-1.381.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.425
r_dihedral_angle_4_deg17.349
r_dihedral_angle_3_deg11.827
r_dihedral_angle_1_deg5.716
r_angle_refined_deg1.461
r_mcangle_it1.335
r_mcbond_it0.833
r_mcbond_other0.824
r_angle_other_deg0.811
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.425
r_dihedral_angle_4_deg17.349
r_dihedral_angle_3_deg11.827
r_dihedral_angle_1_deg5.716
r_angle_refined_deg1.461
r_mcangle_it1.335
r_mcbond_it0.833
r_mcbond_other0.824
r_angle_other_deg0.811
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5660
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms41

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction