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Crystallization of lipid A transporter MsbA from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 MsbA purified in detergent micelles (UDM/FA231) is mixed with lipid A prior to crystallization and mixed 1: 1 with well solution 20 mM Tris-Hcl (pH 7.5) and 15-20 5 PEG 300 . Crystals appeared in month (approx.)
Crystal Properties Matthews coefficient Solvent content 5.71 78.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.052 α = 90 b = 154.819 β = 90 c = 228.886 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2016-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.127085 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.8 50.01 84.9 0.136 0.148 0.057 0.893 10 5 60504 -3 68.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 82 0.136 0.057 4.1
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 3B5W 2.8 50.01 57572 2963 82.87 0.27104 0.26951 0.2769 0.30071 0.3043 RANDOM 116.187
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] 6.23 8.18 -14.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.818 r_dihedral_angle_3_deg 17.222 r_long_range_B_refined 14.354 r_long_range_B_other 14.35 r_dihedral_angle_4_deg 13.494 r_scangle_other 10.834 r_mcangle_it 10.578 r_mcangle_other 10.577 r_dihedral_angle_1_deg 7.2 r_mcbond_other 6.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.818 r_dihedral_angle_3_deg 17.222 r_long_range_B_refined 14.354 r_long_range_B_other 14.35 r_dihedral_angle_4_deg 13.494 r_scangle_other 10.834 r_mcangle_it 10.578 r_mcangle_other 10.577 r_dihedral_angle_1_deg 7.2 r_mcbond_other 6.933 r_mcbond_it 6.932 r_scbond_it 6.84 r_scbond_other 6.839 r_angle_refined_deg 1.368 r_angle_other_deg 0.974 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 8894 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing