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Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DTE PDB ENTRY 3DTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 281 20% PEG 3350, 0.2M Potassium fluoride, pH 7.5, VAPOR DIFFUSION, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.26 α = 90 b = 52.672 β = 90 c = 63.221 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 3.24 40 97.7 0.095 13.1 4.5 4827 89
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) 3.24 3.42 97.9 0.598 2.2 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3DTE 3.24 19.83 4581 222 96.82 0.22853 0.22627 0.2318 0.27702 0.2732 RANDOM 75.982
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] 0.04 -0.12 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_3_deg 17.24 r_dihedral_angle_4_deg 14.23 r_dihedral_angle_1_deg 4.469 r_angle_refined_deg 0.867 r_mcangle_it 0.801 r_mcbond_it 0.732 r_angle_other_deg 0.673 r_scangle_it 0.399 r_scbond_it 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_3_deg 17.24 r_dihedral_angle_4_deg 14.23 r_dihedral_angle_1_deg 4.469 r_angle_refined_deg 0.867 r_mcangle_it 0.801 r_mcbond_it 0.732 r_angle_other_deg 0.673 r_scangle_it 0.399 r_scbond_it 0.314 r_symmetry_vdw_other 0.265 r_nbd_refined 0.257 r_nbd_other 0.219 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.19 r_symmetry_vdw_refined 0.165 r_nbtor_other 0.093 r_xyhbond_nbd_other 0.082 r_mcbond_other 0.058 r_chiral_restr 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling