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Human Carbonic Anhydrase XII mimic in complex with veralipride
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, HANGING DROP 8 296 2.8 M ammonium sulfate, 100 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.123 α = 90 b = 41.559 β = 104.103 c = 71.84 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 EIGER2 X 9M 2023-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 1.5 40.89 97.3 0.084 0.093 0.997 10.6 5 37695
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 1.5 1.53 93.3 0.616 0.7 0.822 2.2 4.3
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 1.5 40.89 37661 1958 96.865 0.167 0.1656 0.1664 0.1922 0.1919 16.827
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] -0.506 -0.521 0.757 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 7.319 r_lrange_it 5.133 r_lrange_other 5.132 r_scangle_it 3.89 r_scangle_other 3.889 r_scbond_it 2.596 r_scbond_other 2.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.782 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 7.319 r_lrange_it 5.133 r_lrange_other 5.132 r_scangle_it 3.89 r_scangle_other 3.889 r_scbond_it 2.596 r_scbond_other 2.595 r_mcangle_other 2.423 r_mcangle_it 2.419 r_angle_refined_deg 1.793 r_mcbond_it 1.632 r_mcbond_other 1.621 r_angle_other_deg 1.463 r_symmetry_nbd_refined 0.327 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.234 r_symmetry_nbd_other 0.212 r_nbd_other 0.197 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.093 r_metal_ion_refined 0.092 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 232 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing