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Crystal structure of the monomeric, cleaved form of the Pore-Forming Toxin Monalysin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJT PBD entry 4MJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1M sodium acetate, pH 4.6, 0.13M zinc acetate, 0.6-1.1M ammonium acetate, 2-7% PEG800, 1.5mM HgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.844 α = 90 b = 117.649 β = 90 c = 150.584 γ = 90
Symmetry Space Group P 21 21 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 1.7 30 100 0.093 12.9 6.7 126982 126982 14.11
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 1.7 1.79 100 0.445 3.9 6.8 18400
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PBD entry 4MJT 1.7 29.78 126982 126896 6374 99.82 0.1804 0.1791 0.1856 0.2046 0.2117 RANDOM 17.56
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] 4.8666 -8.8768 4.0102
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.34 t_omega_torsion 3.58 t_angle_deg 0.93 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.34 t_omega_torsion 3.58 t_angle_deg 0.93 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7476 Nucleic Acid Atoms Solvent Atoms 1318 Heterogen Atoms 68
Software Software Software Name Purpose BUSTER refinement