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Human carbonic anhydrase II complexed with 2-hydroselenobenzoic acid
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 8 293 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.39 α = 90 b = 41.31 β = 104.139 c = 72.61 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 1.27 41.14 86.6 0.048 0.052 0.999 18.75 5.64 55534
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 1.27 1.31 36.4 0.397 0.481 0.809 2.2 3.03
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 1.272 41.14 55534 2739 86.572 0.115 0.1134 0.1525 0.1706 15.798
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] -0.336 -0.368 1.72 -1.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 26.159 r_dihedral_angle_3_deg 12.412 r_dihedral_angle_1_deg 6.833 r_rigid_bond_restr 6.046 r_scangle_it 4.792 r_scangle_other 4.791 r_lrange_it 4.377 r_lrange_other 4.368 r_scbond_it 4.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.489 r_dihedral_angle_4_deg 26.159 r_dihedral_angle_3_deg 12.412 r_dihedral_angle_1_deg 6.833 r_rigid_bond_restr 6.046 r_scangle_it 4.792 r_scangle_other 4.791 r_lrange_it 4.377 r_lrange_other 4.368 r_scbond_it 4.177 r_scbond_other 4.175 r_mcangle_other 2.739 r_mcangle_it 2.708 r_mcbond_it 2.25 r_mcbond_other 2.161 r_angle_refined_deg 2.024 r_angle_other_deg 1.532 r_symmetry_nbd_refined 0.311 r_nbd_refined 0.273 r_nbd_other 0.234 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.14 r_chiral_restr 0.123 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.05 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2057 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing