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Full-length S95A ClbP bound to N-acyl-D-asparagine analog
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, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol 2 LIPIDIC CUBIC PHASE 295 Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 5.5 mM (4-(4-bromophenyl)butanoyl)-D-asparagine plus 3.5 parts 0.1M tris pH 7.4, 28%(v/v) PEG400, 100 mM Li2SO4, 1.2% (w/v) myo-inositol
Crystal Properties Matthews coefficient Solvent content 3.88 68.26 3.88 68.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.686 α = 90 b = 96.686 β = 90 c = 182.736 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 PILATUS 6M-F 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.92020 APS 24-ID-C
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 2.3 46.74 99.81 0.362 0.3731 0.08917 0.997 8.89 17.2 39268 33.75
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 2.3 2.382 99.63 2.781 2.872 0.7095 0.697 1.32 15.9
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 2.3 46.74 39236 1964 99.81 0.1914 0.1917 0.219 0.2187 57.39
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 15.708 f_angle_d 0.8938 f_chiral_restr 0.0514 f_plane_restr 0.0079 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3394 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 195
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing