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Zinc finger region of human TET1 in complex with CpG DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HP3 PDB entry 4hp3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 25% PEG-3350, 0.2 M ammonium acetate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.6 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.502 α = 90 b = 31.951 β = 121.82 c = 65.414 γ = 90
Symmetry Space Group C 1 2 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) Rrim I (All) 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 1.85 36.72 98.3 0.038 0.044 0.023 1 22.1 3.6 11082
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 95.7 0.423 0.494 0.252 0.872 3.8 676
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4hp3 1.85 36.72 10543 539 98.13 0.2033 0.2016 0.2154 0.235 0.2446 36.226
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] -1.09 0.3 0.37 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.548 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_4_deg 6.978 r_dihedral_angle_1_deg 4.799 r_mcangle_it 1.74 r_angle_refined_deg 1.455 r_angle_other_deg 1.336 r_mcbond_it 1.188 r_mcbond_other 1.187 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.548 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_4_deg 6.978 r_dihedral_angle_1_deg 4.799 r_mcangle_it 1.74 r_angle_refined_deg 1.455 r_angle_other_deg 1.336 r_mcbond_it 1.188 r_mcbond_other 1.187 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 348 Nucleic Acid Atoms 486 Solvent Atoms 58 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing