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Wide inward-open liganded UraA in complex with a conformation-selective synthetic nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8OMZ the unliganded UraA(G320P)-Sy45 structure was used for molecular replacement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 291 50 mM Tris, 50 mM magnesium acetate, 0.1% Benzamidine, 40% (v/v) PEG400, 1 mM uracil
Crystal Properties Matthews coefficient Solvent content 3.73 67.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.25 α = 90 b = 116.82 β = 100.485 c = 94.3 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 DECTRIS PILATUS 2M-F 2020-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.01 49.42 63.6 0.159 0.172 0.998 10.14 6.8 23194 50.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.09 0.322 0.35 0.958
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.7 49.42 1.37 19362 989 97.94 0.2724 0.2711 0.2763 0.2944 0.2862 52.08
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 20.1407 f_angle_d 0.4529 f_chiral_restr 0.0369 f_plane_restr 0.0034 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7935 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 219
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing