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Crystal structure of SAM-dependent O-methyltransferase (TM0748) from Thermotoga maritima at 1.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5 293 40% MPD, 0.1M sodium acetate trihydrate, pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.253 α = 90 b = 74.992 β = 90 c = 143.701 γ = 90
Symmetry Space Group I 2 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 315 flat mirror 2003-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.65 35.93 95.9 0.055 17.4 4.7 40334 40334 31.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 78.8 0.433 1.9 2.2 4754
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1I9G 1.65 35.93 38297 2036 95.7 0.15918 0.15768 0.18762 0.2257 RANDOM 27.161
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] 0.67 1.31 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.186 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_4_deg 12.53 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.32 r_scbond_it 2.522 r_mcangle_it 1.759 r_angle_refined_deg 1.409 r_mcbond_it 0.959 r_angle_other_deg 0.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.186 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_4_deg 12.53 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.32 r_scbond_it 2.522 r_mcangle_it 1.759 r_angle_refined_deg 1.409 r_mcbond_it 0.959 r_angle_other_deg 0.755 r_symmetry_hbond_refined 0.26 r_symmetry_vdw_other 0.245 r_xyhbond_nbd_refined 0.236 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.2 r_nbd_other 0.181 r_chiral_restr 0.083 r_nbtor_other 0.082 r_bond_refined_d 0.015 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 2090 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling