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Crystal structure of native NalD at resolution of 2.9, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 tacsimate,sodium citrate tribasic dihydrate, polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.676 α = 90 b = 127.602 β = 90 c = 265.42 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 2.89 50 99.6 0.09 32.46 9.3 47656
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 2.89 3 98.7 0.69 3.5 9.3
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 5DAJ 2.89 30 45176 2411 98.81 0.19699 0.19397 0.2002 0.25214 0.2445 RANDOM 91.563
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] -3.19 5.37 -2.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 86.361 r_dihedral_angle_2_deg 35.307 r_sphericity_bonded 20.775 r_dihedral_angle_3_deg 20.434 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_1_deg 4.549 r_rigid_bond_restr 3.946 r_angle_other_deg 1.745 r_angle_refined_deg 1.515 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 86.361 r_dihedral_angle_2_deg 35.307 r_sphericity_bonded 20.775 r_dihedral_angle_3_deg 20.434 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_1_deg 4.549 r_rigid_bond_restr 3.946 r_angle_other_deg 1.745 r_angle_refined_deg 1.515 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12623 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing