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Crystal structure of human carbonic anhydrase II in complex with the inhibitor Aprocitentan
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 8 296 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.501 α = 90 b = 41.867 β = 104.66 c = 73.097 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 2024-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 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 1.65 41.87 90.1 0.094 0.115 0.995 9.4 5.6 27212
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 1.65 1.68 99.9 0.537 0.653 0.915 2.3 5.6
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 (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 1.65 36.05 24667 1335 86.11 0.28977 0.28765 0.2949 0.32847 0.3305 RANDOM 19.068
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] 0.08 -0.01 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 7.644 r_long_range_B_other 4.717 r_long_range_B_refined 4.707 r_scangle_other 3.156 r_mcangle_other 2.423 r_mcangle_it 2.421 r_scbond_it 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.66 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 7.644 r_long_range_B_other 4.717 r_long_range_B_refined 4.707 r_scangle_other 3.156 r_mcangle_other 2.423 r_mcangle_it 2.421 r_scbond_it 2.06 r_scbond_other 2.059 r_angle_refined_deg 1.618 r_mcbond_it 1.594 r_mcbond_other 1.582 r_angle_other_deg 1.305 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing