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Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NTE PDB ENTRY 2NTE CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES
15% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.979 α = 90 b = 67.466 β = 99.2 c = 86.783 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 2007-02-12 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 Merge I (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 2.01 50 82.4 0.045 0.063 16.77 3.3 28268 2 2 39.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 30.4 0.578 0.696 1.22 2.6 1032
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2NTE CHAIN A 2.2 30 2 2 23629 1255 95.01 0.22605 0.22237 0.2851 0.29772 0.3377 RANDOM 21.983
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] 3.48 -1.85 -2.37 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_1_deg 6.891 r_scangle_it 1.751 r_angle_refined_deg 1.283 r_scbond_it 1.267 r_mcangle_it 0.839 r_angle_other_deg 0.832 r_mcbond_it 0.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_1_deg 6.891 r_scangle_it 1.751 r_angle_refined_deg 1.283 r_scbond_it 1.267 r_mcangle_it 0.839 r_angle_other_deg 0.832 r_mcbond_it 0.687 r_symmetry_vdw_other 0.255 r_xyhbond_nbd_refined 0.207 r_nbd_refined 0.199 r_nbd_other 0.187 r_xyhbond_nbd_other 0.181 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.18 r_symmetry_vdw_refined 0.167 r_mcbond_other 0.118 r_nbtor_other 0.083 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3295 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 27
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction HKL-2000 data scaling