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2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHD PDB ENTRY 1XHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH 7.5, 2% MPD, 20% (w/v) PEG 3350;
Cryo: paratone., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.089 α = 90 b = 127.089 β = 90 c = 76.732 γ = 120
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 Beryllium lenses 2011-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2 30 99.9 0.107 29.5 9.7 47926 47926 -3 19.1
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 2 2.03 100 0.61 3.8 9.5 2398
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XHD 2 29.36 45299 45299 2416 99.87 0.21439 0.21439 0.21158 0.2183 0.26663 0.2678 RANDOM 42.179
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 0.45 0.89 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_4_deg 12.229 r_dihedral_angle_3_deg 11.971 r_long_range_B_refined 6.838 r_long_range_B_other 6.628 r_dihedral_angle_1_deg 3.762 r_scangle_other 3.322 r_scbond_it 2.412 r_scbond_other 2.397 r_mcangle_it 2.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_4_deg 12.229 r_dihedral_angle_3_deg 11.971 r_long_range_B_refined 6.838 r_long_range_B_other 6.628 r_dihedral_angle_1_deg 3.762 r_scangle_other 3.322 r_scbond_it 2.412 r_scbond_other 2.397 r_mcangle_it 2.199 r_mcangle_other 2.198 r_angle_refined_deg 1.619 r_mcbond_it 1.506 r_mcbond_other 1.505 r_angle_other_deg 0.785 r_chiral_restr 0.102 r_gen_planes_refined 0.018 r_gen_planes_other 0.017 r_bond_refined_d 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5152 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 6
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing