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Structure of Rad14 in complex with acetylaminoanthracene-C8-guanine containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3D
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.065 α = 90 b = 53.065 β = 90 c = 130.323 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 2015-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 49.2 100 0.19 9.8 4.4 28204
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 1.9 2 98 0.68 1.4 3.2
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 5A3D 1.9 53.12 26848 1361 99.58 0.21849 0.21721 0.2279 0.24392 0.2548 RANDOM 48.079
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] 0.26 0.26 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.325 r_dihedral_angle_4_deg 19.884 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_1_deg 5.942 r_mcangle_it 2.284 r_angle_refined_deg 1.987 r_mcbond_it 1.307 r_mcbond_other 1.298 r_angle_other_deg 1.288 r_scbond_it 1.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.325 r_dihedral_angle_4_deg 19.884 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_1_deg 5.942 r_mcangle_it 2.284 r_angle_refined_deg 1.987 r_mcbond_it 1.307 r_mcbond_other 1.298 r_angle_other_deg 1.288 r_scbond_it 1.194 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms 1164 Solvent Atoms 55 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing