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Crystal structure of quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293.15 mixing 1 ml of protein solution at 9 mg/ml, 1 ml of reservoir solution containing 0.1 M sodium acetate pH 4.6 and 1.75 M ammonium sulfate, and allowing the drop to equilibrate against 1 ml of reservoir solution by the hanging drop method
Crystal Properties Matthews coefficient Solvent content 4.17 70.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.59 α = 90 b = 87.59 β = 90 c = 63.81 γ = 120
Symmetry Space Group P 31 2 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 CCD RAYONIX MX225HE 2011-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 63.81 99.4 0.086 0.09 0.027 0.998 15.8 11 19458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 100 0.903 0.947 0.283 0.778 10.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 48.83 1.34 19432 987 99.31 0.1974 0.1955 0.1949 0.2348 0.2339
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.015 f_angle_d 1.144 f_chiral_restr 0.076 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 965 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling iMOSFLM data reduction PHASER phasing