☰ Navigation Tabs
Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-M
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 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.284 α = 90 b = 64.582 β = 90 c = 77.836 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 1.55 30 95.6 0.057 13.7 6.5 28938 -3 21.6
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) 1.55 1.61 70.1 0.35 2.4 3.2 2080
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 1.55 21.15 28871 1456 95.64 0.202 0.2 0.1998 0.235 0.2374 RANDOM 20.374
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] -0.89 0.13 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.72 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_4_deg 11.817 r_dihedral_angle_1_deg 5.506 r_scangle_it 2.288 r_scbond_it 1.585 r_angle_refined_deg 1.239 r_mcangle_it 0.998 r_mcbond_it 0.645 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.72 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_4_deg 11.817 r_dihedral_angle_1_deg 5.506 r_scangle_it 2.288 r_scbond_it 1.585 r_angle_refined_deg 1.239 r_mcangle_it 0.998 r_mcbond_it 0.645 r_nbtor_refined 0.306 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 60
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MX data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing