☰ Navigation Tabs
Crystal structure of the DNMT3A ADD domain in complex with histone H3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A1A PDB ENTRY 3A1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.57 65.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.547 α = 90 b = 68.547 β = 90 c = 109.95 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315 mirrors 2008-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.292 32.721 98.3 0.082 15 24.1 12159 12159 1 1
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 2.292 2.38 86.9 0.428 15.5
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 PDB ENTRY 3A1A 2.292 32.72 11534 576 98.14 0.19344 0.19198 0.1898 0.22408 0.2181 RANDOM 43.685
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] 2.16 2.16 -4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.229 r_dihedral_angle_4_deg 17.577 r_dihedral_angle_3_deg 16.946 r_dihedral_angle_1_deg 4.854 r_scangle_it 3.57 r_scbond_it 2.282 r_angle_refined_deg 1.501 r_mcangle_it 1.277 r_mcbond_it 0.797 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.229 r_dihedral_angle_4_deg 17.577 r_dihedral_angle_3_deg 16.946 r_dihedral_angle_1_deg 4.854 r_scangle_it 3.57 r_scbond_it 2.282 r_angle_refined_deg 1.501 r_mcangle_it 1.277 r_mcbond_it 0.797 r_nbtor_refined 0.304 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.205 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1173 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing