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Crystal structure of mouse DNA methyltransferase 1 with AdoMet
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 297 PEG 3350, NaCl, TCEP, pH 9.0, vapor diffusion, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.995 α = 90 b = 97.139 β = 90 c = 130.794 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX225HE mirror 2010-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 3.09 50 99.8 0.086 11.6 4.8 32007 -3 64.8
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) 3.1 3.15 100 0.331 5 1591
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3AV4 3.09 43.14 31970 1626 0.1945 0.1913 0.1978 0.2546 0.2615 RANDOM 56.404
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] 4.6712 0.6469 -5.3181
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.18 t_omega_torsion 3.04 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.18 t_omega_torsion 3.04 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9079 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose SCALEPACK data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction DENZO data reduction BUSTER refinement