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Zinc finger region of human TET3 in complex with CpG DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 30% PEG-1500, 0.2 M sodium chloride, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.4 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.616 α = 90 b = 54.744 β = 103.53 c = 40.228 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.57 39.11 99.7 0.07 0.042 0.998 10.4 3.6 16318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 99.8 1.07 0.665 0.464 1.1 3.5 812
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 4HP3 1.57 39.11 16301 807 99.62 0.2164 0.2146 0.2192 0.2525 0.2622 RANDOM 28.058
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] 0.37 0.79 -2.39 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.986 r_dihedral_angle_4_deg 24.509 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 5.984 r_mcangle_it 2.42 r_angle_refined_deg 1.667 r_mcbond_other 1.623 r_mcbond_it 1.619 r_angle_other_deg 1.451 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.986 r_dihedral_angle_4_deg 24.509 r_dihedral_angle_3_deg 11.924 r_dihedral_angle_1_deg 5.984 r_mcangle_it 2.42 r_angle_refined_deg 1.667 r_mcbond_other 1.623 r_mcbond_it 1.619 r_angle_other_deg 1.451 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 324 Nucleic Acid Atoms 486 Solvent Atoms 85 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing