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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 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.19 α = 90 b = 53.41 β = 90 c = 63.42 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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97618 ESRF ID29
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 3.5 40 99.4 0.102 0.077 8.1 3.5 4071 63
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) 3.5 3.69 99.4 0.48 0.364 2 3.6 579
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 3.5 20 3842 181 99.16 0.24451 0.24131 0.233 0.3142 0.2987 RANDOM 66.089
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] 3.02 -4.09 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.675 r_dihedral_angle_3_deg 19.353 r_dihedral_angle_4_deg 10.656 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.073 r_mcangle_it 1.047 r_mcbond_it 0.917 r_angle_other_deg 0.706 r_scangle_it 0.54 r_scbond_it 0.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.675 r_dihedral_angle_3_deg 19.353 r_dihedral_angle_4_deg 10.656 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.073 r_mcangle_it 1.047 r_mcbond_it 0.917 r_angle_other_deg 0.706 r_scangle_it 0.54 r_scbond_it 0.407 r_nbd_refined 0.282 r_xyhbond_nbd_refined 0.262 r_nbd_other 0.23 r_symmetry_vdw_other 0.208 r_nbtor_refined 0.198 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_other 0.129 r_nbtor_other 0.094 r_mcbond_other 0.074 r_chiral_restr 0.051 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 1838 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DNA data collection XDS data reduction SCALA data scaling deduced phasing