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Crystal structure of carbonic anhydrase II with methyl 4-methylsulfanyl-3-sulfamoyl-benzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)
Crystal Properties Matthews coefficient Solvent content 2.03 38.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.314 α = 90 b = 41.169 β = 104.4 c = 72.026 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 2021-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976200 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.39 40.985 97.6 0.036 0.044 0.017 24.2 7 47284 47284
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.47 94.9 0.377 0.377 0.443 0.168 1.9 6.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.39 39.94 42563 4706 97.23 0.1464 0.1416 0.1443 0.1896 0.1799 RANDOM 21.784
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] 1.22 0.98 -0.45 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.712 r_sphericity_free 29.4 r_dihedral_angle_4_deg 23.657 r_sphericity_bonded 17.192 r_dihedral_angle_3_deg 11.638 r_dihedral_angle_1_deg 7.016 r_rigid_bond_restr 4.969 r_angle_refined_deg 2.023 r_chiral_restr 0.133 r_bond_refined_d 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.712 r_sphericity_free 29.4 r_dihedral_angle_4_deg 23.657 r_sphericity_bonded 17.192 r_dihedral_angle_3_deg 11.638 r_dihedral_angle_1_deg 7.016 r_rigid_bond_restr 4.969 r_angle_refined_deg 2.023 r_chiral_restr 0.133 r_bond_refined_d 0.014 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 37
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building MOLREP phasing XDS data reduction