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Minocycline bound structure of bacterial efflux pump.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M MES pH6.5, 0.21 M NaCl, 11.5% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.557 α = 90 b = 145.409 β = 90 c = 175.612 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 PILATUS 6M 2015-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 50 99.3 0.162 0.997 11.5 9 96991
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 99.3 1.241 0.617 8.9
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-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 5EN5 2.5 50 92224 4767 99.86 0.19601 0.19337 0.1991 0.24768 0.2495 RANDOM 52.249
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] 1.44 -2.88 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.008 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.863 r_long_range_B_other 9.15 r_long_range_B_refined 9.145 r_scangle_other 6.724 r_dihedral_angle_1_deg 6.62 r_mcangle_other 6.078 r_mcangle_it 6.077 r_scbond_it 4.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.008 r_dihedral_angle_4_deg 19.475 r_dihedral_angle_3_deg 15.863 r_long_range_B_other 9.15 r_long_range_B_refined 9.145 r_scangle_other 6.724 r_dihedral_angle_1_deg 6.62 r_mcangle_other 6.078 r_mcangle_it 6.077 r_scbond_it 4.248 r_scbond_other 4.248 r_mcbond_it 3.963 r_mcbond_other 3.949 r_angle_refined_deg 1.655 r_angle_other_deg 0.998 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16886 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling PHASER phasing