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Crystal structure of type-I restriction-modification system methylation subunit (MM_0429) from Methanosarchina mazei.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 Sodium acetate trihydrate pH 4.6, 25% PEG 3350,0.2M Ammonium Acetate,0.05M Magnesium Sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.648 α = 90 b = 80.648 β = 90 c = 179.973 γ = 90
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 2009-08-20 SINGLE WAVELENGTH 2 1 100 CCD ADSC QUANTUM 315 2009-03-06
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A 2 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 25 100 0.098 0.117 25.8 10.6 37205 37205
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.55 2.59 100 0.816 0.882 3 10.7 1916
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 2.55 25 37097 1858 99.65 0.214 0.213 0.2092 0.242 0.2339 RANDOM 51.862
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] 5.82 5.82 -11.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.963 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.204 r_scbond_it 1.424 r_angle_refined_deg 1.355 r_mcangle_it 1.018 r_mcbond_it 0.545 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.963 r_dihedral_angle_4_deg 19.83 r_dihedral_angle_3_deg 19.287 r_dihedral_angle_1_deg 6.458 r_scangle_it 2.204 r_scbond_it 1.424 r_angle_refined_deg 1.355 r_mcangle_it 1.018 r_mcbond_it 0.545 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7863 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing SHELXD phasing