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Structure of the thermolabile hemolysin from Vibrio alginolyticus (apo form)
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 was grown in a drop containing 1.0 ul of protein solution (10 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 200 mM NDSB201) and 1.0 ul of reservoir solution (0.1 M Tris pH 8.5, 20.5% polyethylene glycol 4000, 20% polyethylene glycol 400, and 0.1 M MgCl2).
Crystal Properties Matthews coefficient Solvent content 1.99 38.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.932 α = 90 b = 71.238 β = 101.32 c = 83.645 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 2019-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97876 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 1.809 53.783 98.8 0.08 0.087 0.033 0.998 12.9 6.9 68600
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 1.809 1.84 98.1 0.709 0.767 0.288 0.863 2.3 6.9
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 6JKZ 1.81 53.78 68495 3351 98.8 0.181 0.18 0.204 0.2106 RANDOM 36.7
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] 3.563 1.514 -8.303 4.74
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.15 t_omega_torsion 3.6 t_angle_deg 0.93 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 17.15 t_omega_torsion 3.6 t_angle_deg 0.93 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 6150 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 169
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing