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Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-D
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, SITTING DROP 7 298 5% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.45 α = 90 b = 64.89 β = 90 c = 78.48 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 2008-01-23 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 1.29 40 97.7 0.057 15.54 6.9 51669 -3 20.179
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) 1.29 1.42 91.9 0.475 3.9 6.5 11984
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 2Q6M 1.29 19.31 51602 2594 98.14 0.175 0.174 0.1722 0.203 0.2029 RANDOM 19.21
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] 0.88 -0.62 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_4_deg 14.676 r_dihedral_angle_3_deg 12.256 r_sphericity_free 6.805 r_sphericity_bonded 5.858 r_dihedral_angle_1_deg 5.714 r_scangle_it 3.768 r_scbond_it 2.881 r_mcangle_it 2.178 r_rigid_bond_restr 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.516 r_dihedral_angle_4_deg 14.676 r_dihedral_angle_3_deg 12.256 r_sphericity_free 6.805 r_sphericity_bonded 5.858 r_dihedral_angle_1_deg 5.714 r_scangle_it 3.768 r_scbond_it 2.881 r_mcangle_it 2.178 r_rigid_bond_restr 1.82 r_mcbond_it 1.493 r_angle_refined_deg 1.454 r_nbtor_refined 0.308 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 43
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection XDS data reduction MOLREP phasing