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Crystal structure of NalD, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 Tacsimate, Sodium citrate tribasic dihydrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.75 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.639 α = 90 b = 128.137 β = 90 c = 266.063 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 CCD ADSC QUANTUM 315r 2012-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.65 50 99.6 0.1 17.4 7.4 61847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 99.4 0.8 3.8 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.65 30 58632 3122 99.34 0.21335 0.21048 0.2117 0.2661 0.2643 RANDOM 87.04
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] -4.52 2.23 2.28
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 69.054 r_sphericity_bonded 41.922 r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 17.15 r_long_range_B_refined 11.88 r_long_range_B_other 11.759 r_scangle_other 10.254 r_mcangle_it 9.823 r_mcangle_other 9.823
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 69.054 r_sphericity_bonded 41.922 r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 17.337 r_dihedral_angle_3_deg 17.15 r_long_range_B_refined 11.88 r_long_range_B_other 11.759 r_scangle_other 10.254 r_mcangle_it 9.823 r_mcangle_other 9.823 r_scbond_it 7.969 r_scbond_other 7.969 r_mcbond_other 7.287 r_mcbond_it 7.286 r_rigid_bond_restr 5.832 r_dihedral_angle_1_deg 4.734 r_angle_other_deg 1.485 r_angle_refined_deg 1.305 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 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 12585 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing