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Minocycline binding to the deep binding pocket of AcrB-G619P
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, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000, 0.0012M MINOCYCLINE
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.281 α = 90 b = 161.008 β = 90 c = 245.457 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 PILATUS3 S 6M 2014-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 SOLEIL PROXIMA 1
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 2.35 49.36 100 0.163 0.181 0.077 0.994 8.6 5.4 240294
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 2.35 2.39 99.9 1.968 2.177 0.923 0.408 1 5.5
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-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 2.35 49.36 228104 12078 99.97 0.2324 0.2311 0.2334 0.2572 0.2584 RANDOM 44.408
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] -2.35 2.74 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.878 r_dihedral_angle_4_deg 15.719 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_1_deg 5.101 r_angle_refined_deg 1.17 r_angle_other_deg 1.018 r_chiral_restr 0.032 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 29.878 r_dihedral_angle_4_deg 15.719 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_1_deg 5.101 r_angle_refined_deg 1.17 r_angle_other_deg 1.018 r_chiral_restr 0.032 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 25984 Nucleic Acid Atoms Solvent Atoms 1188 Heterogen Atoms 882
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction