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Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant)
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, HANGING DROP 9 293 PEG 3350, NaCl, TCEP, Na-citrate
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.998 α = 90 b = 97.804 β = 90 c = 130.319 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 MX300HE 2014-10-17 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) Rrim I (All) Rpim I (All) 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 3.26 50 97.5 0.19 0.219 0.106 5.4 4.4 26720 73.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.26 3.32 96.4 0.748 0.355 4.4
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 3.27 50 23536 1255 90.36 0.2061 0.2032 0.205 0.2627 0.2594 RANDOM 87.666
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] -3.31 -1.97 5.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.599 r_dihedral_angle_4_deg 18.064 r_dihedral_angle_3_deg 16.858 r_mcangle_it 6.252 r_dihedral_angle_1_deg 6.204 r_mcbond_it 3.773 r_mcbond_other 3.768 r_angle_other_deg 2.311 r_angle_refined_deg 1.415 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.599 r_dihedral_angle_4_deg 18.064 r_dihedral_angle_3_deg 16.858 r_mcangle_it 6.252 r_dihedral_angle_1_deg 6.204 r_mcbond_it 3.773 r_mcbond_other 3.768 r_angle_other_deg 2.311 r_angle_refined_deg 1.415 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9108 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction Coot model building MOLREP phasing HKL-2000 data reduction