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Structure of UbiX Y169F in complex with a covalent adduct formed between reduced FMN and dimethylallyl monophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 12% PEG 3350, 150mM sodium thiocyanate, and 100mM Tris pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.26 α = 90 b = 142.26 β = 90 c = 142.26 γ = 90
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 PSI PILATUS 6M 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.45 50.3 99.9 0.028 15.7 5.5 40068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.49 0.356 2.4 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.45 50.3 40068 2066 99.82 0.10469 0.1026 0.103 0.14723 0.1467 RANDOM 21.217
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 r_dihedral_angle_2_deg 38.865 r_sphericity_free 26.056 r_dihedral_angle_4_deg 19.614 r_sphericity_bonded 13.407 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.593 r_scangle_other 5.928 r_scbond_it 5.654 r_scbond_other 5.598 r_rigid_bond_restr 5.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.865 r_sphericity_free 26.056 r_dihedral_angle_4_deg 19.614 r_sphericity_bonded 13.407 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.593 r_scangle_other 5.928 r_scbond_it 5.654 r_scbond_other 5.598 r_rigid_bond_restr 5.406 r_long_range_B_refined 5.007 r_long_range_B_other 5.006 r_mcangle_it 3.208 r_mcangle_other 3.208 r_mcbond_it 2.871 r_mcbond_other 2.87 r_angle_refined_deg 2.228 r_angle_other_deg 1.304 r_chiral_restr 0.462 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1545 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing