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Xenon for tunnelling analysis of the efflux pump component OprN.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 291 100 mM sodium acetate, 1 M sodium formate, 10 % PEG 4000 (w/v)
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 256.412 α = 90 b = 256.412 β = 90 c = 81.395 γ = 90
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 2016-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.771 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.5 181 100 0.19 0.07 4.5 6.7 91716
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 5IUY 2.5 49.42 86977 4736 99.95 0.17491 0.17133 0.1823 0.23938 0.246 RANDOM 40.791
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.197 r_sphericity_free 30.38 r_dihedral_angle_4_deg 22.44 r_dihedral_angle_3_deg 17.54 r_sphericity_bonded 15.522 r_scangle_other 8.684 r_long_range_B_refined 7.696 r_scbond_it 7.686 r_scbond_other 7.685 r_long_range_B_other 7.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.197 r_sphericity_free 30.38 r_dihedral_angle_4_deg 22.44 r_dihedral_angle_3_deg 17.54 r_sphericity_bonded 15.522 r_scangle_other 8.684 r_long_range_B_refined 7.696 r_scbond_it 7.686 r_scbond_other 7.685 r_long_range_B_other 7.662 r_rigid_bond_restr 7.113 r_mcangle_other 6.949 r_mcangle_it 6.941 r_mcbond_it 5.737 r_mcbond_other 5.712 r_dihedral_angle_1_deg 5.26 r_angle_refined_deg 2.176 r_angle_other_deg 1.132 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10311 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing