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Cholera holotoxin with an A-subunit Y30S mutation, Crystal form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S5B CTY30S Form 3 structure (PDB ID 1S5B)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 PEG 3350, sodium citrate, galactose, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.055 α = 90 b = 111.904 β = 90 c = 124.656 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 CCD CUSTOM-MADE 2003-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0000 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 38.92 95.5 0.068 25.3 6.1 81705 81705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 73.2 0.291 3.37 6191
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 (All) 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 CTY30S Form 3 structure (PDB ID 1S5B) 1.75 30.71 77516 77516 4074 95.54 0.16278 0.16278 0.16129 0.19149 0.1974 RANDOM 15.561
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 r_dihedral_angle_1_deg 6.391 r_scangle_it 2.156 r_mcangle_it 1.755 r_scbond_it 1.293 r_angle_refined_deg 1.227 r_mcbond_it 1.063 r_angle_other_deg 0.708 r_symmetry_vdw_other 0.338 r_nbd_other 0.263 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.391 r_scangle_it 2.156 r_mcangle_it 1.755 r_scbond_it 1.293 r_angle_refined_deg 1.227 r_mcbond_it 1.063 r_angle_other_deg 0.708 r_symmetry_vdw_other 0.338 r_nbd_other 0.263 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.161 r_nbtor_other 0.086 r_symmetry_vdw_refined 0.083 r_chiral_restr 0.077 r_metal_ion_refined 0.069 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5693 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing