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Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with terretonin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 0.27 M magnesium chloride, 20% w/v PEG 3350, 0.2 M sodium chloride, 1.5% trimethylamine N-oxide dihydrate
Crystal Properties Matthews coefficient Solvent content 1.94 36.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.651 α = 81.929 b = 72.281 β = 84.88 c = 78.455 γ = 70.354
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 EIGER X 4M 2021-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.07 Photon Factory BL-1A
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 2.1 48.24 97.6 0.065 0.996 7.3 2.1 57878 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 96.2 0.632 0.871 1.8 2.1
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 7EYR 2.1 48.24 2.01 57781 1999 97.4 0.2073 0.2056 0.2062 0.2558 0.256 34.97
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 16.6346 f_angle_d 0.5667 f_chiral_restr 0.0408 f_plane_restr 0.0047 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8465 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing