☰ Navigation Tabs
Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB - Y424F mutant with impaired DNA repair activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 100 MM MES, 5% PEG400, PH 6.0,
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.183 α = 90 b = 94.441 β = 90 c = 103.579 γ = 90
Symmetry Space Group P 2 21 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 6M MIRRORS 2014-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96863 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 69.79 99.51 0.2 0.963 5.3 5.3 19657 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 100 0.75 2.1 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DJA 2.5 69.79 18586 1031 99.51 0.18388 0.18071 0.23961 0.2352 RANDOM 30.516
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] 0.37 0.34 -0.71
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.756 r_dihedral_angle_2_deg 29.245 r_dihedral_angle_4_deg 15.551 r_sphericity_bonded 13.222 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 5.039 r_long_range_B_other 3.539 r_long_range_B_refined 3.538 r_mcangle_it 2.711 r_mcangle_other 2.711
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.756 r_dihedral_angle_2_deg 29.245 r_dihedral_angle_4_deg 15.551 r_sphericity_bonded 13.222 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 5.039 r_long_range_B_other 3.539 r_long_range_B_refined 3.538 r_mcangle_it 2.711 r_mcangle_other 2.711 r_scangle_other 2.532 r_rigid_bond_restr 2.346 r_mcbond_it 1.935 r_mcbond_other 1.928 r_scbond_it 1.92 r_scbond_other 1.919 r_angle_refined_deg 1.303 r_angle_other_deg 0.97 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3916 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction PHASER phasing