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Crystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with 5-amino-1,3,4-thiadiazole-2-sulfonamide inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 12% (w/v) PEG 1.5K, 100 mM di-basic ammonium citrate, 1 mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.84 α = 90 b = 136.92 β = 90.04 c = 166.27 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 210r 2014-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.5 166.27 99.8 0.047 0.056 0.03 16.6 3.3 64612 64612
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.7 0.315 0.315 0.382 0.212 2.3 3.1 9445
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YGF 2.5 29.912 1.35 64588 3277 99.82 0.229 0.2269 0.2468 0.2721 0.2889 52.3148
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.291 f_angle_d 1.337 f_chiral_restr 0.052 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14347 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing ADSC data collection Coot model building