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Structure of UbiX in complex with oxidised prenylated FMN (radical)
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 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.79 α = 90 b = 141.79 β = 90 c = 141.79 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 2013-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
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 1.61 42.75 99.9 0.024 20.1 5.6 29027
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) 1.61 1.65 100 0.335 2.5 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 1.61 42.75 29027 1541 99.82 0.14493 0.1436 0.1575 0.17095 0.1848 RANDOM 22.876
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 40.011 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 13.027 r_long_range_B_refined 6.498 r_long_range_B_other 6.496 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.306 r_scbond_it 3.549 r_scbond_other 3.538 r_mcangle_it 3.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.011 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 13.027 r_long_range_B_refined 6.498 r_long_range_B_other 6.496 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.306 r_scbond_it 3.549 r_scbond_other 3.538 r_mcangle_it 3.244 r_mcangle_other 3.243 r_angle_refined_deg 2.431 r_mcbond_it 2.319 r_mcbond_other 2.311 r_angle_other_deg 1.734 r_chiral_restr 0.276 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 r_bond_other_d 0.004 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 127 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing