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Crystal structure of human carbonic anhydrase II with 3-(3-((1-(2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl)-1H-1,2,3-triazol-4-yl)methyl)ureido)benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.304 α = 90 b = 41.199 β = 104.319 c = 72.181 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 PIXEL DECTRIS PILATUS3 S 6M 2020-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0001 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.28 41.2 99.7 0.033 0.039 0.021 0.999 24.9 6.1 62015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.3 97.2 0.192 0.217 0.139 0.972 6.1 5.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4FIK 1.28 39.966 62000 3152 99.634 0.154 0.1525 0.1597 0.1754 0.1782 14.394
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] 0.211 -0.228 -0.221 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.315 r_dihedral_angle_4_deg 22.596 r_dihedral_angle_3_deg 11.709 r_dihedral_angle_1_deg 7.052 r_lrange_it 4.519 r_lrange_other 4.518 r_scangle_it 3.908 r_scangle_other 3.907 r_scbond_it 2.584 r_scbond_other 2.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.315 r_dihedral_angle_4_deg 22.596 r_dihedral_angle_3_deg 11.709 r_dihedral_angle_1_deg 7.052 r_lrange_it 4.519 r_lrange_other 4.518 r_scangle_it 3.908 r_scangle_other 3.907 r_scbond_it 2.584 r_scbond_other 2.583 r_mcangle_it 2.068 r_mcangle_other 2.067 r_angle_refined_deg 1.994 r_angle_other_deg 1.481 r_mcbond_it 1.453 r_mcbond_other 1.414 r_symmetry_xyhbond_nbd_refined 0.551 r_symmetry_nbd_refined 0.278 r_nbd_refined 0.247 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.18 r_nbd_other 0.164 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.071 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing