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Catalytic fragment of Cholix toxin from Vibrio Cholerae in complex with inhibitor GP-P
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 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.525 α = 90 b = 64.685 β = 90 c = 84.226 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 1.65 30 92.3 0.1 8.7 6.1 22167 -3 15.36
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) 1.65 1.71 65.4 0.296 3.5 4.2 1538
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 1.65 22.03 22125 1142 92.06 0.169 0.167 0.1669 0.202 0.2016 RANDOM 13.225
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.13 r_dihedral_angle_3_deg 12.108 r_dihedral_angle_4_deg 11.951 r_dihedral_angle_1_deg 5.796 r_scangle_it 3.514 r_scbond_it 2.283 r_angle_refined_deg 1.407 r_mcangle_it 1.216 r_mcbond_it 0.797 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.13 r_dihedral_angle_3_deg 12.108 r_dihedral_angle_4_deg 11.951 r_dihedral_angle_1_deg 5.796 r_scangle_it 3.514 r_scbond_it 2.283 r_angle_refined_deg 1.407 r_mcangle_it 1.216 r_mcbond_it 0.797 r_nbtor_refined 0.308 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1552 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MX data collection HKL-2000 data reduction HKL-2000 data scaling