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Crystal structure of YojK mutant in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VM0 7VM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M Ammonium acetate, 0.1 M HEPES (pH 7.5) and 25% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.753 α = 90 b = 79.979 β = 91.1 c = 99.244 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 Bruker PHOTON II 2022-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.498 62.35 99.76 0.277 12.8 9.51 25482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.498 2.587 0.535
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 MOLECULAR REPLACEMENT THROUGHOUT 7VM0 2.5 62.35 24117 1264 99.74 0.1834 0.1787 0.1871 0.2725 0.274 RANDOM 30.116
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] 1.56 -0.11 0.61 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.69 r_dihedral_angle_3_deg 18.811 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_1_deg 8.034 r_angle_refined_deg 1.698 r_angle_other_deg 1.242 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.69 r_dihedral_angle_3_deg 18.811 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_1_deg 8.034 r_angle_refined_deg 1.698 r_angle_other_deg 1.242 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6223 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SAINT data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing