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Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 NANODROP, 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG 300, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.86 α = 90 b = 83.86 β = 90 c = 159.2 γ = 120
Symmetry Space Group P 31 2 1
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 325 mm CCD Flat mirror (vertical focusing) 2007-01-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97908, 0.97879 SSRL BL11-1
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 2 29.975 99.6 0.044 21.1 4.9 44338 32.8
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 2 2.05 99.6 0.325 3.09 4.9 3115
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 (All) 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 MAD THROUGHOUT 2 29.16 44263 2229 99.53 0.167 0.167 0.165 0.176 0.201 0.2085 RANDOM 43.522
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] -0.17 -0.08 -0.17 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 15.593 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 6.653 r_scangle_it 6.477 r_scbond_it 4.761 r_mcangle_it 2.677 r_mcbond_it 1.881 r_angle_refined_deg 1.352 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 15.593 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 6.653 r_scangle_it 6.477 r_scbond_it 4.761 r_mcangle_it 2.677 r_mcbond_it 1.881 r_angle_refined_deg 1.352 r_angle_other_deg 0.78 r_mcbond_other 0.588 r_symmetry_vdw_refined 0.226 r_symmetry_vdw_other 0.192 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.186 r_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3287 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 88
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction SHELXD phasing autoSHARP phasing