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Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-I
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 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.467 α = 90 b = 64.898 β = 90 c = 91.756 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 1.32 50 91 0.121 5.8 6.7 46297 -3 8.4
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) 1.32 1.37 87.4 0.282 5.6 5.2 4380
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 1.32 18.73 46202 2338 92.01 0.152 0.15 0.1495 0.174 0.1734 RANDOM 9.887
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.807 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_4_deg 11.264 r_dihedral_angle_1_deg 5.972 r_sphericity_free 4.282 r_scangle_it 2.919 r_sphericity_bonded 2.532 r_scbond_it 2.19 r_mcangle_it 1.541 r_angle_refined_deg 1.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.807 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_4_deg 11.264 r_dihedral_angle_1_deg 5.972 r_sphericity_free 4.282 r_scangle_it 2.919 r_sphericity_bonded 2.532 r_scbond_it 2.19 r_mcangle_it 1.541 r_angle_refined_deg 1.342 r_rigid_bond_restr 1.109 r_mcbond_it 1.048 r_nbtor_refined 0.309 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.13 r_xyhbond_nbd_refined 0.097 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1554 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection HKL-2000 data reduction HKL-2000 data scaling