☰ Navigation Tabs
Structure of the pre-pore AhlB of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet AhlB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.2 M ammonium phosphate
0.1 M Tris pH 8.5
50 % (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.661 α = 90 b = 178.184 β = 90 c = 485.581 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M-F 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 2.55 39.55 100 0.188 0.122 6.6 6.4 165574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.73 100 0.751 2.7 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SeMet AhlB 2.55 39.55 156934 8380 99.8 0.19497 0.19052 0.27844 0.2511 RANDOM 39.264
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] 1.6 1.53 -3.13
RMS Deviations Key Refinement Restraint Deviation r_mcbond_other 87.013 r_mcbond_it 87.01 r_long_range_B_refined 72.764 r_long_range_B_other 72.763 r_scbond_it 71.545 r_scbond_other 70.685 r_mcangle_it 69.2 r_mcangle_other 69.199 r_scangle_other 61.63 r_dihedral_angle_2_deg 40.419
RMS Deviations Key Refinement Restraint Deviation r_mcbond_other 87.013 r_mcbond_it 87.01 r_long_range_B_refined 72.764 r_long_range_B_other 72.763 r_scbond_it 71.545 r_scbond_other 70.685 r_mcangle_it 69.2 r_mcangle_other 69.199 r_scangle_other 61.63 r_dihedral_angle_2_deg 40.419 r_dihedral_angle_4_deg 21.033 r_dihedral_angle_3_deg 18.195 r_dihedral_angle_1_deg 6.182 r_angle_refined_deg 1.568 r_angle_other_deg 0.983 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 24746 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing