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Crystal structure of human carbonic anhydrase XII mimic in complex with sonepiprazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 296 2.5 M ammonium sulfate, 100 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.112 α = 90 b = 41.459 β = 104.135 c = 71.888 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 2023-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 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 1.8 40.87 100 0.092 0.097 0.998 22.5 17.5 22560
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 1.8 1.84 99.8 0.152 0.161 0.995 13.7 18.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 40.87 22548 1145 99.938 0.12 0.1161 0.1394 0.1954 0.2059 15.445
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] 0.346 -0.072 -0.172 -0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_3_deg 14.459 r_dihedral_angle_4_deg 13.408 r_dihedral_angle_1_deg 7.161 r_lrange_other 5.275 r_lrange_it 5.187 r_scangle_it 4.71 r_scangle_other 4.708 r_scbond_it 3.798 r_scbond_other 3.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_3_deg 14.459 r_dihedral_angle_4_deg 13.408 r_dihedral_angle_1_deg 7.161 r_lrange_other 5.275 r_lrange_it 5.187 r_scangle_it 4.71 r_scangle_other 4.708 r_scbond_it 3.798 r_scbond_other 3.796 r_mcangle_it 3.196 r_mcangle_other 3.114 r_rigid_bond_restr 2.694 r_mcbond_it 2.405 r_mcbond_other 2.404 r_angle_refined_deg 1.823 r_angle_other_deg 1.47 r_symmetry_nbd_refined 0.305 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_other 0.203 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.061 r_metal_ion_refined 0.061 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2055 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing