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Full-length wildtype ClbP inhibited by hexanoyl-D-asparagine boronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 295 Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 11 mM (S)-N-(3-amino-3-oxo-1-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)propyl)hexanamide plus 3.5 parts 0.1M tris pH 7.2, 25%(v/v) PEG400, 200 mM Li2SO4
Crystal Properties Matthews coefficient Solvent content 3.88 68.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.718 α = 90 b = 96.718 β = 90 c = 183.382 γ = 90
Symmetry Space Group P 42 21 2
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 EIGER X 16M 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.98 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.7 45.58 99.88 0.2575 0.2702 0.08088 0.996 8.06 10.9 24663 48.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 99.92 1.887 1.975 0.5802 0.534 11.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7MDE 2.7 45.58 24644 1231 99.88 0.1926 0.1937 0.2359 0.2386 57.88
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 21.0649 f_angle_d 0.9222 f_chiral_restr 0.0518 f_plane_restr 0.0082 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3315 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction PHENIX phasing