3G5T

Crystal structure of trans-aconitate 3-methyltransferase from yeast


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Protein solution (8 mg/ml MSE Protein, 0.040 M NaCl, 0.00024 M TCEP, 0.001 M SAM, 0.008 M Trans-aconitic acid, 0.0045 M HEPES pH 7.0) mixed in a 1:1 ratio with the Well solution (24% PEG 8000, 2% DMSO, 0.05 M HEPES pH 7.5). Cryoprotected with 23% PEG 8000, 2% DMSO, 0.001 M SAM, 0.0085 M Trans-aconitate, 0.05 M HEPES pH 7.5, 19% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5251.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.834α = 90
b = 91.891β = 90
c = 104.269γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97886APS21-ID-D

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
11.1195097.40.10432.62812.5134803
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)
1.1191.1677.30.3224.4646.510548

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.11934.47134502675198.1760.1210.120.137RANDOM12.564
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]
-0.1610.020.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.672
r_dihedral_angle_4_deg21.26
r_sphericity_free15.644
r_dihedral_angle_3_deg12.732
r_dihedral_angle_1_deg7.074
r_sphericity_bonded6.338
r_scangle_it5.801
r_scbond_it4.455
r_mcangle_it3.212
r_rigid_bond_restr2.402
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.672
r_dihedral_angle_4_deg21.26
r_sphericity_free15.644
r_dihedral_angle_3_deg12.732
r_dihedral_angle_1_deg7.074
r_sphericity_bonded6.338
r_scangle_it5.801
r_scbond_it4.455
r_mcangle_it3.212
r_rigid_bond_restr2.402
r_mcbond_it2.263
r_angle_refined_deg2.262
r_mcbond_other1.103
r_angle_other_deg0.88
r_chiral_restr0.154
r_bond_refined_d0.03
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4891
Nucleic Acid Atoms
Solvent Atoms541
Heterogen Atoms75

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling