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Crystal Structure of the Ring Domain of RNF168
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 291 1.5 M NaMalonate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.706 α = 90 b = 49.706 β = 90 c = 110.149 γ = 90
Symmetry Space Group P 43 21 2
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 RIGAKU SATURN A200 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 2.12 45.31 99.4 0.1238 40.1 53.39 8436 8384
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 2.12 2.22 99.7 0.6495 5.17 54.28 1047
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 S-SAD coupled with molecular replacement THROUGHOUT 3FL2 2.12 45.49 8384 7964 420 100 0.1887 0.1887 0.18734 0.1945 0.21477 0.2184 RANDOM 33.912
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] 1.38 1.38 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.781 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_1_deg 5.952 r_angle_refined_deg 2.423 r_chiral_restr 0.215 r_mcbond_it 0.055 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.781 r_dihedral_angle_3_deg 20.948 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_1_deg 5.952 r_angle_refined_deg 2.423 r_chiral_restr 0.215 r_mcbond_it 0.055 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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_mcangle_it r_scbond_it 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 830 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 16
Software Software Software Name Purpose CrystalClear data collection SHELXD phasing MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling