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Crystal structure of carbonic anhydrase II with methyl 4-phenylsulfanyl-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, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.08 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.269 α = 90 b = 41.295 β = 104.4 c = 71.903 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 EIGER X 4M 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 Merge I (Observed) Rrim I (All) Rpim 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 1.42 40.94 96.4 0.04 0.048 0.018 0.999 23 7.1 43783
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.5 95 0.376 0.428 0.158 0.949 7.2
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 1.42 40.94 39554 4216 95.99 0.15338 0.14805 0.1656 0.20558 0.2081 RANDOM 19.275
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] 1.85 0.11 2.08 -3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_sphericity_free 34.627 r_sphericity_bonded 25.767 r_dihedral_angle_4_deg 21.707 r_dihedral_angle_3_deg 13.175 r_rigid_bond_restr 9.691 r_dihedral_angle_1_deg 7.364 r_long_range_B_refined 4.516 r_scbond_it 4.129 r_mcangle_it 2.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_sphericity_free 34.627 r_sphericity_bonded 25.767 r_dihedral_angle_4_deg 21.707 r_dihedral_angle_3_deg 13.175 r_rigid_bond_restr 9.691 r_dihedral_angle_1_deg 7.364 r_long_range_B_refined 4.516 r_scbond_it 4.129 r_mcangle_it 2.835 r_mcbond_it 2.451 r_angle_refined_deg 1.985 r_chiral_restr 0.147 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2037 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing