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Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-G
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 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.16 α = 90 b = 64.87 β = 90 c = 78.41 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 1.28 40 98.6 0.052 20.48 6.9 52851 -3 20.832
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) 1.28 1.41 97.2 0.316 6 6.6 12948
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 1.28 18.93 52847 2666 98.67 0.182 0.181 0.1777 0.205 0.201 RANDOM 19.505
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] 0.08 -0.05 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 13.156 r_sphericity_free 6.389 r_dihedral_angle_1_deg 5.747 r_sphericity_bonded 5.699 r_scangle_it 3.714 r_scbond_it 2.818 r_mcangle_it 2.186 r_rigid_bond_restr 1.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 13.156 r_sphericity_free 6.389 r_dihedral_angle_1_deg 5.747 r_sphericity_bonded 5.699 r_scangle_it 3.714 r_scbond_it 2.818 r_mcangle_it 2.186 r_rigid_bond_restr 1.647 r_mcbond_it 1.493 r_angle_refined_deg 1.396 r_nbtor_refined 0.315 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.152 r_symmetry_vdw_refined 0.145 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1539 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection XDS data reduction MOLREP phasing