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Crystal structure of putative DNA modification methyltransferase encoded within prophage Cp-933R (E.coli)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 294 0.1M Sodium/potassium phosphate pH 6.2, 20% PEG 1000, 200mM Sodium chloride, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.436 α = 90 b = 79.436 β = 90 c = 126.539 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 ADSC QUANTUM 315 Mirrors 2009-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 1.75 50 100 0.062 9.5 8 47134 -5 26.51
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 1.75 1.81 100 0.656 1.6 6.2
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 1.75 20 45597 1460 99.99 0.18411 0.18299 0.1834 0.21914 0.2189 RANDOM 35.469
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] 0.89 0.44 0.89 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.564 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_4_deg 14.18 r_scangle_it 6.031 r_dihedral_angle_1_deg 5.757 r_scbond_it 4.435 r_mcangle_it 4.277 r_mcbond_it 2.898 r_angle_refined_deg 1.519 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.564 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_4_deg 14.18 r_scangle_it 6.031 r_dihedral_angle_1_deg 5.757 r_scbond_it 4.435 r_mcangle_it 4.277 r_mcbond_it 2.898 r_angle_refined_deg 1.519 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.197 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.158 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 2771 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 13
Software Software Software Name Purpose MAR345 data collection SHELXD phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling