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X-ray crystal structure of R28D mutant of the human NBS1 FHA-BRCT1-BRCT2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 26BE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 Trisbicine, sodium nitrate, dibasic sodium phosphate, ammonium sulfate, ethylene glycol, PEG 8,000.
Crystal Properties Matthews coefficient Solvent content 6.1 79.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.721 α = 90 b = 182.384 β = 90 c = 122.635 γ = 90
Symmetry Space Group C 2 2 21
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 2M-F 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.84 48.46 99.9 0.999 22.6 13.4 42051
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.95 0.894
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.84 48.453 42022 2083 99.907 0.186 0.1845 0.1887 0.2235 0.2211 89.222
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] -6.219 8.067 -1.848
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.624 r_lrange_other 18.624 r_dihedral_angle_3_deg 18.551 r_scangle_it 15.825 r_scangle_other 15.823 r_dihedral_angle_6_deg 14.152 r_mcangle_it 13.361 r_mcangle_other 13.36 r_scbond_it 10.956 r_scbond_other 10.955
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.624 r_lrange_other 18.624 r_dihedral_angle_3_deg 18.551 r_scangle_it 15.825 r_scangle_other 15.823 r_dihedral_angle_6_deg 14.152 r_mcangle_it 13.361 r_mcangle_other 13.36 r_scbond_it 10.956 r_scbond_other 10.955 r_dihedral_angle_2_deg 9.663 r_mcbond_it 9.634 r_mcbond_other 9.63 r_dihedral_angle_1_deg 7.779 r_angle_refined_deg 1.96 r_angle_other_deg 0.676 r_symmetry_xyhbond_nbd_refined 0.354 r_nbd_refined 0.242 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.19 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.14 r_ncsr_local_group_1 0.135 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.09 r_symmetry_nbd_refined 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5010 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing