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The crystal structure of a methyltransferase domain from Bacteroides thetaiotaomicron VPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M Ammonium Sulfate,
0.1M Bis-Tris,
25% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.321 α = 90 b = 70.919 β = 90 c = 86.908 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 ADSC QUANTUM 315 Mirror 2008-12-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926, 0.97937 APS 19-ID
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 2.35 40 95.8 0.088 30.7 5.6 11310 11310
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 2.35 2.39 80.9 0.528 2.68 4.8 441
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.36 39.5 10719 10719 535 95.29 0.21694 0.21694 0.21383 0.2255 0.28571 0.2853 RANDOM 42.313
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] -0.13 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.846 r_dihedral_angle_3_deg 21.456 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_1_deg 7.185 r_scangle_it 3.296 r_scbond_it 2.068 r_angle_refined_deg 1.716 r_mcangle_it 1.283 r_mcbond_it 0.657 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.846 r_dihedral_angle_3_deg 21.456 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_1_deg 7.185 r_scangle_it 3.296 r_scbond_it 2.068 r_angle_refined_deg 1.716 r_mcangle_it 1.283 r_mcbond_it 0.657 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1816 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 15
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building RESOLVE model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing