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Room temperature structure of an extradiol ring-cleaving dioxygenase from B.fuscum determined using serial femtosecond crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.8 293 Precipitant added to enzyme solution at 1:1 ratio: 12-14% PEG6000, 0.1-0.14 M calcium chloride, and 0.1 M MES pH 5.8. Crystallization carried out in a tube to produce saturated slurry of micro crystals
Crystal Properties Matthews coefficient Solvent content 2.63 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.57 α = 90 b = 154.86 β = 90 c = 101.8 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 293 PIXEL CS-PAD CXI-2 2015-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.5498 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.38 34.5 99.9 0.81 2.43 26.5 71326
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.47 99.5 0.45 3.42 13
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 FOURIER SYNTHESIS THROUGHOUT 3OJT 2.38 20 67578 3568 99.69 0.1869 0.1845 0.1923 0.2321 0.2375 RANDOM 43.583
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] 0.13 0.66 -0.79
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 2.259 r_mcbond_it 1.511 r_mcbond_other 1.511 r_angle_refined_deg 1.358 r_angle_other_deg 0.816 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11596 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data scaling CrystFEL data reduction