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Crystal structure of human Carbonic anhydrase II in complex with (R)-4-(3-(1-(6-nitropyridin-2-yl)pyrrolidin-3-yl)thioureido)benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FIK 4FIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.32 α = 90 b = 41.17 β = 104.335 c = 71.67 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 PILATUS 6M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.999 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 48 84.1 0.138 0.152 0.984 7.61 5.1 51575
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.32 36.1 0.525 0.617 0.831 2.1 3.38
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 1.283 41.036 51563 2504 84.034 0.158 0.1562 0.166 0.2033 0.2123 18.559
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] -1.934 0.81 -1.312 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.383 r_dihedral_angle_4_deg 19.859 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 7.284 r_rigid_bond_restr 4.221 r_scangle_it 4.14 r_scangle_other 4.139 r_lrange_it 3.981 r_lrange_other 3.98 r_scbond_it 3.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.383 r_dihedral_angle_4_deg 19.859 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 7.284 r_rigid_bond_restr 4.221 r_scangle_it 4.14 r_scangle_other 4.139 r_lrange_it 3.981 r_lrange_other 3.98 r_scbond_it 3.764 r_scbond_other 3.764 r_mcangle_other 2.621 r_mcangle_it 2.6 r_mcbond_it 2.406 r_mcbond_other 2.267 r_angle_refined_deg 2.059 r_angle_other_deg 1.525 r_nbd_refined 0.23 r_metal_ion_refined 0.224 r_symmetry_nbd_other 0.207 r_nbd_other 0.205 r_symmetry_nbd_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.18 r_chiral_restr 0.126 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.021 r_xyhbond_nbd_other 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2045 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing