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Structure of the thermolabile hemolysin from Vibrio alginolyticus (in complex with docosahexaenoic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JKZ 6JKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The crystal of ValTLH in complex with docosahexaenoic acid was grown in a drop containing 1.0 ul of protein solution (6 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300mM NDSB201 with 1.25 mM docosahexaenoic acid) and 1.0 ul of reservoir solution (25% polyethylene glycol 20000, 0.15 M magnesium formate).
Crystal Properties Matthews coefficient Solvent content 2 38.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.671 α = 90 b = 72.13 β = 101.61 c = 83.489 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2021-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.008 81.779 99.9 0.076 0.083 0.032 0.997 14.8 6.7 51148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.008 2.014 0.85 0.927 0.365 0.865 2
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 6JKZ 2.01 81.779 50957 2527 99.9 0.193 0.191 0.1982 0.225 0.2301 RANDOM 47.97
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] 8.0406 0.2934 -10.9844 2.9437
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.69 t_omega_torsion 3.25 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.69 t_omega_torsion 3.25 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6242 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 51
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing