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Three dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294 0.15 M MgCl2, 0.1 M NaAce (pH 5.5), 15% PEG 4000,PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO)
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.567 α = 62.61 b = 76.701 β = 79.07 c = 78.868 γ = 72.89
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 2024-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
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 1.45 44.41 96.6 0.069 10.2 3.6 158363 8.297
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 1.45 1.47 94.8 0.309 3.9 3.5
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 1.45 44.41 150307 8053 96.63 0.18549 0.18425 0.1936 0.20861 0.2169 RANDOM 12.564
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] -0.29 -0.17 0.1 -0.14 -0.02 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 17.449 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 7.496 r_long_range_B_refined 4.269 r_long_range_B_other 4.208 r_scangle_other 3.006 r_scbond_it 2.054 r_scbond_other 2.054 r_mcangle_it 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 17.449 r_dihedral_angle_3_deg 12.947 r_dihedral_angle_1_deg 7.496 r_long_range_B_refined 4.269 r_long_range_B_other 4.208 r_scangle_other 3.006 r_scbond_it 2.054 r_scbond_other 2.054 r_mcangle_it 2.002 r_mcangle_other 2.002 r_angle_refined_deg 1.987 r_angle_other_deg 1.505 r_mcbond_it 1.309 r_mcbond_other 1.308 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 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 8332 Nucleic Acid Atoms Solvent Atoms 768 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling