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BDM88855 inhibitor bound to the transmembrane domain of AcrB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 291 0.05M ADA, PH 6.6, 0.13-0.2M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.008M BDM88855
Crystal Properties Matthews coefficient Solvent content 3.87 68.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.126 α = 90 b = 159.647 β = 90 c = 245.499 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 2.6 49.1 99.9 0.226 0.235 0.063 0.998 9.5 13.9 176116
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 2.6 2.64 99.7 2.081 2.158 0.572 0.597 14
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 MOLECULAR REPLACEMENT THROUGHOUT 5JMN 2.6 49.05 167178 8846 99.86 0.2377 0.2365 0.2372 0.2625 0.2615 RANDOM 55.257
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] -0.38 0.3 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.622 r_dihedral_angle_4_deg 13.789 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 4.772 r_angle_refined_deg 1.172 r_angle_other_deg 1.022 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.622 r_dihedral_angle_4_deg 13.789 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 4.772 r_angle_refined_deg 1.172 r_angle_other_deg 1.022 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25930 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 599
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing