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Human Carbonic Anhydrase II in complex with veralipride
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 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.4 α = 90 b = 41.62 β = 104.494 c = 72.33 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 2021-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.97170 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 1.34 35.8 99.7 0.058 0.063 0.999 17.37 6.1 54690
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 1.34 1.38 98.1 0.679 0.769 0.727 2.29 4.59
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 1.342 35.8 54690 2667 99.741 0.118 0.1156 0.1323 0.1564 0.1654 16.987
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] -0.248 -0.441 2.134 -1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_4_deg 25.601 r_dihedral_angle_3_deg 11.299 r_dihedral_angle_1_deg 7.156 r_rigid_bond_restr 6.122 r_scangle_it 5.401 r_scangle_other 5.4 r_lrange_other 5.232 r_lrange_it 5.227 r_scbond_it 4.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_4_deg 25.601 r_dihedral_angle_3_deg 11.299 r_dihedral_angle_1_deg 7.156 r_rigid_bond_restr 6.122 r_scangle_it 5.401 r_scangle_other 5.4 r_lrange_other 5.232 r_lrange_it 5.227 r_scbond_it 4.597 r_scbond_other 4.595 r_mcangle_other 3.299 r_mcangle_it 3.257 r_mcbond_it 2.798 r_mcbond_other 2.685 r_angle_refined_deg 2.096 r_angle_other_deg 1.548 r_nbd_refined 0.24 r_nbd_other 0.208 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.177 r_chiral_restr 0.123 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.058 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2050 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing