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Structure of UbiX in complex with oxidised FMN and dimethylallyl monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other This structure was solved using difference fourier
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 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.9 α = 90 b = 141.9 β = 90 c = 141.9 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 2014-07-12 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) R Merge 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 1.71 70.95 100 0.027 18.7 6.7 24314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.71 1.75 100 0.298 2.8
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 FOURIER SYNTHESIS THROUGHOUT This structure was solved using difference fourier 1.71 70.95 24314 1295 99.92 0.1392 0.13744 0.1512 0.17231 0.1834 RANDOM 23.416
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 38.353 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 11.893 r_long_range_B_refined 6.489 r_long_range_B_other 6.488 r_dihedral_angle_1_deg 6.202 r_scangle_other 5.161 r_scbond_it 3.472 r_scbond_other 3.461 r_mcangle_it 3.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.353 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 11.893 r_long_range_B_refined 6.489 r_long_range_B_other 6.488 r_dihedral_angle_1_deg 6.202 r_scangle_other 5.161 r_scbond_it 3.472 r_scbond_other 3.461 r_mcangle_it 3.054 r_mcangle_other 3.053 r_mcbond_it 2.257 r_mcbond_other 2.256 r_angle_refined_deg 2.119 r_angle_other_deg 0.996 r_chiral_restr 0.285 r_bond_refined_d 0.025 r_gen_planes_refined 0.016 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing