3TCV

Crystal structure of a GCN5-related N-acetyltransferase from Brucella melitensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PZJPDB entry 3pzj

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289BrabA.17403.a.A1 OS01078 at 28.7 mg/mL against JCSG+ condition A3 0.2 M ammonium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 223197a3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6353.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.49α = 90
b = 66.86β = 107.51
c = 91.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002011-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.03322CLSI08ID-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
11.755097.10.06713.813.75973058008-324.153
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)
11.751.882.30.4532.653.34397

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 3pzj1.755058008291897.180.16260.16120.1895RANDOM20.4328
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]
1.07-0.13-1.320.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.854
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg12.039
r_dihedral_angle_1_deg5.771
r_angle_refined_deg1.388
r_angle_other_deg0.843
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.854
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg12.039
r_dihedral_angle_1_deg5.771
r_angle_refined_deg1.388
r_angle_other_deg0.843
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3587
Nucleic Acid Atoms
Solvent Atoms625
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction