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Zinc finger of human CXXC4 in complex with CpG DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished model of related protein-DNA complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 30% PEG-1500, 5% MPD, 0.2 M sodium chloride, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.4 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.983 α = 70.98 b = 40.29 β = 86.43 c = 57.76 γ = 67.83
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 2013-06-19 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 2.1 27.24 97.2 0.061 0.081 0.054 0.995 10.1 2.1 13389
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 2.1 2.16 92.6 0.597 0.82 0.559 0.653 1.8 1057
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished model of related protein-DNA complex 2.1 27.2 12637 750 97.13 0.2132 0.211 0.2481 0.2597 thin resolution shells (sftools) 45.818
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] 2.36 0.7 -0.78 -1.17 0.4 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_4_deg 23.25 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 6.769 r_mcangle_it 2.489 r_mcbond_other 1.783 r_mcbond_it 1.781 r_angle_refined_deg 1.554 r_angle_other_deg 1.474 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_4_deg 23.25 r_dihedral_angle_3_deg 11.367 r_dihedral_angle_1_deg 6.769 r_mcangle_it 2.489 r_mcbond_other 1.783 r_mcbond_it 1.781 r_angle_refined_deg 1.554 r_angle_other_deg 1.474 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 668 Nucleic Acid Atoms 972 Solvent Atoms 30 Heterogen Atoms 11
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction