4DGT

Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630 crystallized with magnesium formate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T32SwissModel generated model based on PDB ENTRY 3T32 structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729325% PEG 3350, 2M Mg Formate, pH 7.0, vapor diffusion, hanging drop, temperature 20K, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9235.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.744α = 90
b = 55.624β = 91.25
c = 79.133γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2011-07-06SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.979APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.555099.50.0740.074193.69959899100-313
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5894.10.4070.4072.32.54608

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSwissModel generated model based on PDB ENTRY 3T32 structure1.55509948999012494799.520.14910.14910.14750.1809RANDOM17.2009
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]
-0.040.08-0.330.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.168
r_dihedral_angle_3_deg13.837
r_dihedral_angle_4_deg10.781
r_dihedral_angle_1_deg5.998
r_angle_other_deg2.428
r_angle_refined_deg1.817
r_chiral_restr0.117
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.168
r_dihedral_angle_3_deg13.837
r_dihedral_angle_4_deg10.781
r_dihedral_angle_1_deg5.998
r_angle_other_deg2.428
r_angle_refined_deg1.817
r_chiral_restr0.117
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6274
Nucleic Acid Atoms
Solvent Atoms878
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
CCP4phasing