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Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EG2 PDB ENTRY 1EG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 lithium sulfate, HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.428 α = 90 b = 130.07 β = 90 c = 67.216 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.94 28 99.8 0.038 22.5 23315 23268 21.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.01 99.8 0.167 6.5 2292
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EG2 1.94 28.13 23257 23210 2289 99.6 0.22 0.22 0.2199 0.246 0.245 RANDOM 27.8
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] -1.05 3.88 -2.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 2.98 c_mcangle_it 2.06 c_scbond_it 2.05 c_mcbond_it 1.35 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 2.98 c_mcangle_it 2.06 c_scbond_it 2.05 c_mcbond_it 1.35 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2155 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 29
Software Software Software Name Purpose CNS refinement CNS phasing