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crystal structure of human carbonic anhydrase II in complex with sonepiprazole
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 2.11 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.4 α = 90 b = 41.6 β = 104.443 c = 72.19 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 2021-06-03 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 1.32 69.9 98.9 0.066 0.072 0.999 17.28 6.21 57323
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 1.32 1.35 93.9 0.812 0.912 0.71 2.27 4.81
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.32 69.9 57320 2774 98.954 0.115 0.1129 0.1529 0.1647 16.022
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] 0.379 -0.106 -0.178 -0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.8 r_dihedral_angle_4_deg 23.039 r_dihedral_angle_3_deg 12.748 r_dihedral_angle_1_deg 6.785 r_lrange_it 4.713 r_lrange_other 4.666 r_scangle_it 4.151 r_scangle_other 4.15 r_rigid_bond_restr 3.867 r_scbond_it 3.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.8 r_dihedral_angle_4_deg 23.039 r_dihedral_angle_3_deg 12.748 r_dihedral_angle_1_deg 6.785 r_lrange_it 4.713 r_lrange_other 4.666 r_scangle_it 4.151 r_scangle_other 4.15 r_rigid_bond_restr 3.867 r_scbond_it 3.782 r_scbond_other 3.78 r_mcangle_it 2.877 r_mcangle_other 2.875 r_mcbond_other 2.308 r_mcbond_it 2.304 r_angle_refined_deg 2.006 r_angle_other_deg 1.512 r_nbd_refined 0.255 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_nbd_refined 0.202 r_symmetry_nbd_other 0.198 r_nbd_other 0.198 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.176 r_chiral_restr 0.133 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.069 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing