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Structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 2.0M (NH4)2SO4, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.43 α = 90 b = 54.43 β = 90 c = 263.5 γ = 120
Symmetry Space Group P 65 2 2
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 ADSC QUANTUM 210 2009-06-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 47.137 100 0.108 7.6 22767 22767
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 1.8 1.9 100 0.193 7.9 5.9 3197
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2GB4 1.8 19.98 22625 1159 99.99 0.151 0.149 0.1619 0.177 0.1863 RANDOM 8.351
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.226 r_dihedral_angle_4_deg 14.867 r_dihedral_angle_3_deg 11.047 r_dihedral_angle_1_deg 5.869 r_scangle_it 2.951 r_scbond_it 1.75 r_angle_refined_deg 1.285 r_mcangle_it 1.058 r_angle_other_deg 0.836 r_mcbond_it 0.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.226 r_dihedral_angle_4_deg 14.867 r_dihedral_angle_3_deg 11.047 r_dihedral_angle_1_deg 5.869 r_scangle_it 2.951 r_scbond_it 1.75 r_angle_refined_deg 1.285 r_mcangle_it 1.058 r_angle_other_deg 0.836 r_mcbond_it 0.558 r_mcbond_other 0.129 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1697 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 27
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection