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Co-crystal structure of wild-type OYE2 with 2-(prop-1-en-2-yl)pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Bicine-tris (pH = 7.5) , 0.2 M sodium potassium tartrate tetrahydrate, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.927 α = 90 b = 99.198 β = 105.9 c = 119.175 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 S 9M 2024-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
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 3.43 114.61 99.9 0.323 0.352 0.139 0.914 4.7 6.5 29323
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 3.43 3.52 100 0.867 0.943 0.365 0.7 6.7
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 7BN7 3.43 23.31 1.33 29156 1437 99.71 0.2047 0.2016 0.1961 0.2622 0.2535
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 10.151 f_angle_d 1.192 f_chiral_restr 0.061 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12421 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 133
Software Software Software Name Purpose PHENIX refinement Aimless data scaling DIALS data reduction PHENIX phasing