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Crystal structure of AcrB-AcrZ complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C48 PDB ENTRY 4C48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 THE ACRBZ COMPLEX AT 10 MG ML-1 USING SAMPLE BUFFER. 9 MM N-OCTYL-BETA-D-THIOGLUCOPYRANOSIDE (90 MM) WAS MIXED WITH ACRBZ COMPLEX BEFORE THE CRYSTALLISATION TRIALS. THE ACRBZ CRYSTALS WERE GROWN AT 20 C USING THE HANGING-DROPLET VAPOUR DIFFUSION METHOD BY MIXING 4 MICROLITERS OF ACRBZ COMPLEX WITH 2 MICROLITERS OF RESERVOIR SOLUTION (100 MM TRICINE PH: 7.4, 50 MM LITHIUM SULPHATE, 5 MM CADMIUM CHLORIDE HYDRATE, 7 % PEG 3000, 10% GLYCEROL).
Crystal Properties Matthews coefficient Solvent content 4.51 72.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.205 α = 90 b = 146.205 β = 90 c = 543.207 γ = 120
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 2M 2013-01-10 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PIXEL 2013-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24 2 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.69 24.89 94.5 0.13 15.1 10.6 23077 2 148
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 3.69 3.99 94.8 1.17 2.1 10.6
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 PDB ENTRY 4C48 3.7 24.91 21912 1161 94.04 0.34009 0.33906 0.3351 0.36127 0.3523 RANDOM 117.759
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] 3.41 3.41 3.41 -11.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.188 r_dihedral_angle_3_deg 18.157 r_dihedral_angle_4_deg 12.295 r_dihedral_angle_1_deg 7.88 r_mcangle_it 1.582 r_angle_refined_deg 1.398 r_mcbond_it 1.123 r_mcbond_other 1.123 r_scbond_it 1.114 r_angle_other_deg 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.188 r_dihedral_angle_3_deg 18.157 r_dihedral_angle_4_deg 12.295 r_dihedral_angle_1_deg 7.88 r_mcangle_it 1.582 r_angle_refined_deg 1.398 r_mcbond_it 1.123 r_mcbond_other 1.123 r_scbond_it 1.114 r_angle_other_deg 0.818 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8114 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing