☰ Navigation Tabs
Structure of Rad14 in complex with acetylnaphtyl-guanine containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3D PDB ENTRY 5A3D
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 0.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.369 α = 90 b = 53.369 β = 90 c = 131.252 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 PILATUS 2015-09-18 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 2.4 41.4 98 0.19 5.8 3.6 14071
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 2.4 2.5 98 1.39 1.1 3.5
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 PDB ENTRY 5A3D 2.4 53.37 13356 721 98.06 0.25341 0.2511 0.2574 0.29832 0.2991 RANDOM 56.51
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_4_deg 24.2 r_dihedral_angle_3_deg 18.176 r_dihedral_angle_1_deg 6.867 r_mcangle_it 2.087 r_angle_refined_deg 1.603 r_mcbond_it 1.189 r_mcbond_other 1.186 r_angle_other_deg 1.182 r_scbond_it 0.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_4_deg 24.2 r_dihedral_angle_3_deg 18.176 r_dihedral_angle_1_deg 6.867 r_mcangle_it 2.087 r_angle_refined_deg 1.603 r_mcbond_it 1.189 r_mcbond_other 1.186 r_angle_other_deg 1.182 r_scbond_it 0.726 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1856 Nucleic Acid Atoms 1156 Solvent Atoms 6 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing