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Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) by the CXXC Domain of CFP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QMB
Crystallization Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.624 α = 90 b = 75.009 β = 90 c = 125.905 γ = 90
Symmetry Space Group C 2 2 21
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 2010-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 100 8362
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 3QMB 2.1 37.5 8362 420 99.2 0.209 0.207 0.2075 0.258 0.2583 RANDOM 19.21
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] -0.17 0.13 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.595 r_dihedral_angle_4_deg 16.281 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_1_deg 8.157 r_scangle_it 4.679 r_scbond_it 3.559 r_mcangle_it 2.231 r_mcbond_it 1.564 r_angle_refined_deg 1.361 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.595 r_dihedral_angle_4_deg 16.281 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_1_deg 8.157 r_scangle_it 4.679 r_scbond_it 3.559 r_mcangle_it 2.231 r_mcbond_it 1.564 r_angle_refined_deg 1.361 r_chiral_restr 0.078 r_gen_planes_refined 0.022 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 402 Nucleic Acid Atoms 486 Solvent Atoms 33 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement