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Structure of human DNMT1 (601-1600) in complex with Sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 289 5% PEG 4000, 5 mM MgSO4, 50 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60 α = 90 b = 110.77 β = 90 c = 201.26 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 2011-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 2.49 30 98.9 0.078 16.3 4.8 46599 -3 47.7
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 2.49 2.58 96.6 0.59 2.1 4.9
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 3PT9 2.49 30 43542 2177 91.9 0.22 0.22 0.2208 0.272 0.2736 RANDOM 57.3
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] -0.824 17.067 -16.243
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 2.787 c_mcangle_it 2.51 c_scbond_it 1.805 c_mcbond_it 1.435 c_angle_deg 1.4 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 2.787 c_mcangle_it 2.51 c_scbond_it 1.805 c_mcbond_it 1.435 c_angle_deg 1.4 c_improper_angle_d 0.83 c_bond_d 0.006 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 7461 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 160
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling