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1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288 200 mM sodium acetate trihydrate, 30% PEG 4000, 100 mM Tris- HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.77 30.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.298 α = 90 b = 73.087 β = 91.86 c = 42.518 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.56 73.09 87.9 0.075 0.082 0.033 0.996 11.2 5.7 41931 21.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.6 41.5 0.978 1.162 0.612 0.612 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.56 42.496 1.34 41931 3866 86.48 0.1992 0.1963 0.198 0.2271 0.2255 29.2538
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 16.856 f_angle_d 0.859 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1358 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 47
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing