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Crystal structure of the DNA-binding protein DdrC from Deinococcus radiodurans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Tris pH8.0, 1.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.78 67.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.721 α = 90 b = 111.721 β = 90 c = 105.187 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 2M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 49.34 99.9 0.084 0.099 0.051 0.999 12.6 6.4 26653 60.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.8 2.012 2.368 1.219 0.479 1.1 6.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.5 46.251 26627 1333 99.753 0.186 0.1827 0.1844 0.2465 0.2479 Random selection 75.241
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] -1.649 -0.824 -1.649 5.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.197 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_4_deg 13.973 r_lrange_it 6.913 r_lrange_other 6.894 r_scangle_it 6.529 r_scangle_other 5.351 r_mcangle_it 5.304 r_mcangle_other 5.303 r_dihedral_angle_1_deg 4.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.197 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_4_deg 13.973 r_lrange_it 6.913 r_lrange_other 6.894 r_scangle_it 6.529 r_scangle_other 5.351 r_mcangle_it 5.304 r_mcangle_other 5.303 r_dihedral_angle_1_deg 4.824 r_scbond_it 4.615 r_scbond_other 3.861 r_mcbond_other 3.785 r_mcbond_it 3.784 r_angle_refined_deg 1.233 r_angle_other_deg 1.132 r_rigid_bond_restr 0.877 r_nbd_other 0.237 r_symmetry_xyhbond_nbd_refined 0.23 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.179 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.138 r_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3368 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data scaling XDS data reduction