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Crystal structure of bacterial (6-4) photolyase PhrB from in situ serial Laue diffraction
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 MICROBATCH 5.6 294 1.7 mg/mL protein, 9-13% PEG 4000, 6% isopropanol, and 50 mM sodium citrate buffer at pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.7 α = 90 b = 106.8 β = 90 c = 57.3 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 294 CCD RAYONIX MX340-HS KB mirrors 2016-02-11 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1-1.25 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 100 99.3 20.9 15.2 27730 32.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 96.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4dja 2.3 49.68 0.16 27623 1388 99.05 0.1693 0.1658 0.1677 0.2347 0.2356
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.382 f_angle_d 1.127 f_chiral_restr 0.054 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4107 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement Precognition data reduction Epinorm data reduction