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Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF-N65T mutant with andiconin D
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 0.2 M magnesium formate dehydrate, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.813 α = 109.107 b = 50.583 β = 91.294 c = 71.982 γ = 112.859
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 2020-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0 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 2.05 44.6 96.2 0.176 0.971 7.1 4.2 31258 12.15
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 2.05 2.11 95.7 0.455 0.893 3.5 4.2
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 2.05 27.85 1.11 31220 2013 96.08 0.2433 0.2409 0.2399 0.278 0.2788 16.86
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 14.7704 f_angle_d 0.6335 f_chiral_restr 0.0416 f_plane_restr 0.0047 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4303 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing