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Alpha Toxin from Clostridium Absonum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CA1 PDB ENTRY 1CA1 WITH LOOPS OMITTED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 100MM NA-CITRATE 5.6, 30% PEG 4000,200MM AMMONIUM ACETATE, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.42 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.956 α = 90 b = 193.592 β = 90 c = 92.686 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC CCD MIRRORS 2000-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.5 29.784 96.1 0.062 8 2.6 53292
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 2.5 2.63 90 0.195 2 2.4
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 1CA1 WITH LOOPS OMITTED 2.5 29.75 53292 2840 100 0.181 0.178 0.1848 0.237 0.2404 RANDOM 31.89
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.156 r_scangle_it 2.107 r_scbond_it 1.273 r_angle_refined_deg 1.183 r_mcangle_it 1.087 r_angle_other_deg 0.819 r_mcbond_it 0.577 r_nbd_other 0.225 r_symmetry_vdw_other 0.216 r_nbd_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.156 r_scangle_it 2.107 r_scbond_it 1.273 r_angle_refined_deg 1.183 r_mcangle_it 1.087 r_angle_other_deg 0.819 r_mcbond_it 0.577 r_nbd_other 0.225 r_symmetry_vdw_other 0.216 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.145 r_metal_ion_refined 0.106 r_chiral_restr 0.102 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11910 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 20
Software Software Software Name Purpose AMoRE model building REFMAC refinement SCALA data scaling MOLREP phasing CNS phasing COMO phasing AMoRE phasing EPMR phasing XFIT phasing O phasing