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Human Carbonic Anhydrase II in complex with 3,4-dihydro-1H-benzo[c][1,2]oxaborinin-1-ol
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 7 296 1.5 M sodium citrate, 0.1 M Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.45 α = 90 b = 41.44 β = 104.452 c = 72.55 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 0.9717 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 1.43 41.141 99.5 0.059 0.064 0.999 20.26 6.11 45591
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 1.43 1.46 94.9 0.635 0.719 0.786 2.51 4.63
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 1.43 41.141 45590 2153 99.552 0.141 0.139 0.1439 0.1897 0.1896 18.019
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] 2.445 0.911 -1.096 -1.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 23.49 r_rigid_bond_restr 12.967 r_dihedral_angle_3_deg 12.381 r_dihedral_angle_1_deg 7.27 r_lrange_it 4.112 r_lrange_other 4.107 r_scangle_it 3.823 r_scangle_other 3.822 r_mcangle_other 3.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_4_deg 23.49 r_rigid_bond_restr 12.967 r_dihedral_angle_3_deg 12.381 r_dihedral_angle_1_deg 7.27 r_lrange_it 4.112 r_lrange_other 4.107 r_scangle_it 3.823 r_scangle_other 3.822 r_mcangle_other 3.299 r_mcangle_it 3.293 r_scbond_it 3.282 r_scbond_other 3.28 r_mcbond_it 2.48 r_mcbond_other 2.479 r_angle_refined_deg 2.054 r_angle_other_deg 1.5 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.201 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.111 r_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.03 r_symmetry_xyhbond_nbd_other 0.018 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.008 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2053 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing