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Crystal structure of trans-aconitate 3-methyltransferase from yeast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein 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 coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.834 α = 90 b = 91.891 β = 90 c = 104.269 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97886 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.119 50 97.4 0.104 32.628 12.5 134803
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.119 1.16 77.3 0.322 4.464 6.5 10548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.119 34.47 134502 6751 98.176 0.121 0.12 0.2557 0.137 0.2665 RANDOM 12.564
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] -0.161 0.02 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 21.26 r_sphericity_free 15.644 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_1_deg 7.074 r_sphericity_bonded 6.338 r_scangle_it 5.801 r_scbond_it 4.455 r_mcangle_it 3.212 r_rigid_bond_restr 2.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 21.26 r_sphericity_free 15.644 r_dihedral_angle_3_deg 12.732 r_dihedral_angle_1_deg 7.074 r_sphericity_bonded 6.338 r_scangle_it 5.801 r_scbond_it 4.455 r_mcangle_it 3.212 r_rigid_bond_restr 2.402 r_mcbond_it 2.263 r_angle_refined_deg 2.262 r_mcbond_other 1.103 r_angle_other_deg 0.88 r_chiral_restr 0.154 r_bond_refined_d 0.03 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4891 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling