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Zinc finger of human CXXC5 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 6.5 291 30% PEG-5000-MME, 0.2M ammonium sulfate, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.11 α = 90 b = 40.11 β = 90 c = 81.2 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU 2012-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 34.74 100 0.04 0.042 0.012 1 34.9 11.3 8535
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 2.16 100 1.013 1.061 0.315 0.774 2.6 11.1 707
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 2.1 34.74 8107 396 100 0.2202 0.2185 0.2233 0.2537 0.2612 49.286
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] -0.95 -0.48 -0.95 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.866 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 4.429 r_mcangle_it 2.552 r_mcbond_it 1.855 r_mcbond_other 1.852 r_angle_refined_deg 1.744 r_angle_other_deg 1.582 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.866 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 4.429 r_mcangle_it 2.552 r_mcbond_it 1.855 r_mcbond_other 1.852 r_angle_refined_deg 1.744 r_angle_other_deg 1.582 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.015 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 333 Nucleic Acid Atoms 486 Solvent Atoms 12 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data reduction PDB_EXTRACT data extraction XDS data reduction PHASER phasing