☰ Navigation Tabs
Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UYJ PDB ENTRY 1UYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.85 M AMMONIUM DIHYDROGEN PHOSPHATE AND 0.5% (W/V) OCTYLGLUCOSIDE
Crystal Properties Matthews coefficient Solvent content 4.39 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.709 α = 90 b = 123.709 β = 90 c = 127.314 γ = 120
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 RIGAKU SATURN 944 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.4 21.56 100 0.06 12.3 3.7 85072 3
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 2.4 2.49 99.9 0.44 1.2 2.2
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 PDB ENTRY 1UYJ 2.4 21.56 80521 4258 99.48 0.24817 0.2467 0.2175 0.27543 0.2355 RANDOM 52.565
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] 11.39 11.39 -22.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.3 r_dihedral_angle_4_deg 22.391 r_dihedral_angle_3_deg 15.696 r_long_range_B_refined 7.263 r_long_range_B_other 7.262 r_dihedral_angle_1_deg 6.233 r_scangle_other 4.817 r_mcangle_it 4.358 r_mcangle_other 4.358 r_scbond_it 3.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.3 r_dihedral_angle_4_deg 22.391 r_dihedral_angle_3_deg 15.696 r_long_range_B_refined 7.263 r_long_range_B_other 7.262 r_dihedral_angle_1_deg 6.233 r_scangle_other 4.817 r_mcangle_it 4.358 r_mcangle_other 4.358 r_scbond_it 3.139 r_scbond_other 3.135 r_mcbond_it 2.862 r_mcbond_other 2.862 r_angle_refined_deg 1.384 r_angle_other_deg 0.908 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 8443 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling PHASER phasing