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Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with the 1,8-Naphthalimide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q6M PDB ENTRY 2Q6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 15% PEG-8000, 0.02 M KH2PO4, Sitting drop, pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.59 α = 90 b = 64.83 β = 90 c = 91.79 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 MARMOSAIC 225 mm CCD White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM) 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
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 1.19 19.55 99 0.116 18.67 13.96 68749 68071 -3 10.833
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 1.19 1.22 86.9 0.682 5.1 10.15 5012
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 2Q6M 1.191 19.551 1.99 68749 68071 2067 99.04 0.132 0.131 0.1262 0.154 0.1494 Random 8.851
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] 0.475 -1.132 0.64
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.164 f_angle_d 1.344 f_chiral_restr 0.08 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1555 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 15
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Macromolecular data collection XDS data reduction