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STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH C8-aminofluorene- GUANINE CONTAINING DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.22M ammonium nitrate
38% 2-methyl-1,3,-propanediol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.205 α = 90 b = 53.205 β = 90 c = 130.965 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2016-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 49.3 99 0.168 0.995 8.6 7 18314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 93 0.9 1.6 5.6
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 5G32 2.2 49.3 17418 895 99.24 0.2184 0.21651 0.221 0.25555 0.2632 RANDOM 39.035
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] 0.08 0.08 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 16.329 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 5.923 r_long_range_B_refined 3.474 r_long_range_B_other 3.461 r_angle_refined_deg 2.029 r_mcangle_other 1.815 r_mcangle_it 1.812 r_angle_other_deg 1.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 16.329 r_dihedral_angle_3_deg 16.27 r_dihedral_angle_1_deg 5.923 r_long_range_B_refined 3.474 r_long_range_B_other 3.461 r_angle_refined_deg 2.029 r_mcangle_other 1.815 r_mcangle_it 1.812 r_angle_other_deg 1.615 r_scangle_other 1.368 r_mcbond_it 1.105 r_mcbond_other 1.086 r_scbond_it 0.838 r_scbond_other 0.838 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.012 r_bond_other_d 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1861 Nucleic Acid Atoms 579 Solvent Atoms 49 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing