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Crystal structure of putative S-adenosylmethionine dependent methyltransferase from Listeria monocytogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 1M Lithium chloride pH 7.5, 100mM Sodium acetate, 30% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.812 α = 90 b = 92.532 β = 90 c = 99.973 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 90 CCD MAR CCD 165 mm 2008-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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 50 90.7 0.121 5.6 6.3 22700 -0.5
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) 2.35 2.43 99.8 0.43 2.7 5.6
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 2.35 20 19873 670 90.7 0.19235 0.18953 0.1901 0.27618 0.2713 RANDOM 30.473
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] 1.85 0.79 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.831 r_dihedral_angle_3_deg 17.88 r_scangle_it 15.198 r_dihedral_angle_4_deg 14.483 r_scbond_it 12.288 r_mcangle_it 7.886 r_mcbond_it 6.082 r_dihedral_angle_1_deg 6 r_angle_refined_deg 1.199 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.831 r_dihedral_angle_3_deg 17.88 r_scangle_it 15.198 r_dihedral_angle_4_deg 14.483 r_scbond_it 12.288 r_mcangle_it 7.886 r_mcbond_it 6.082 r_dihedral_angle_1_deg 6 r_angle_refined_deg 1.199 r_nbtor_refined 0.295 r_xyhbond_nbd_refined 0.162 r_nbd_refined 0.139 r_symmetry_hbond_refined 0.122 r_symmetry_vdw_refined 0.111 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3639 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 2
Software Software Software Name Purpose MAR345 data collection SHELXD phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling