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Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.2 Mg Chloride, 0.1 M Tris Hydrochloride pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.847 α = 90 b = 74.112 β = 105.23 c = 51.174 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2007-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.68 50 81.2 0.058 17.83 3.3 19640 19640
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.9 26.8 0.527 1.42 2 649
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 MOLECULAR REPLACEMENT THROUGHOUT 1SVX 2 49.39 16373 16373 908 93.49 0.2022 0.2022 0.19857 0.2135 0.26818 0.2691 RANDOM 43.523
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] 3.65 0.15 -1.27 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.384 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_4_deg 10.829 r_dihedral_angle_1_deg 5.428 r_scangle_it 1.856 r_scbond_it 1.246 r_angle_refined_deg 1.227 r_mcangle_it 0.728 r_mcbond_it 0.444 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.384 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_4_deg 10.829 r_dihedral_angle_1_deg 5.428 r_scangle_it 1.856 r_scbond_it 1.246 r_angle_refined_deg 1.227 r_mcangle_it 0.728 r_mcbond_it 0.444 r_nbtor_refined 0.29 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing