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Crystal structure of carbonic anhydrase XII with methyl 4-(2-phenylethylsulfanyl)-3-sulfamoyl-benzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Ammonium Citrate pH 7.0 0.1 M; Ammonium Sulfate 0.2 M; PEG4000 26%
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.338 α = 90 b = 74.222 β = 108.71 c = 91.691 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 2022-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.23 86.84 97.1 0.079 0.093 0.036 0.995 10.8 6.5 273829
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 1.23 1.3 80 0.393 0.499 0.226 0.898 4.5
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 1.23 73.25 246760 27017 97.1 0.14807 0.14459 0.1496 0.17984 0.1803 RANDOM 20.714
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] -0.17 -0.01 0.02 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.253 r_sphericity_free 22.986 r_sphericity_bonded 17.771 r_dihedral_angle_4_deg 16.473 r_dihedral_angle_3_deg 12.097 r_rigid_bond_restr 8.37 r_dihedral_angle_1_deg 7.35 r_long_range_B_refined 5.552 r_scbond_it 5.526 r_mcangle_it 4.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.253 r_sphericity_free 22.986 r_sphericity_bonded 17.771 r_dihedral_angle_4_deg 16.473 r_dihedral_angle_3_deg 12.097 r_rigid_bond_restr 8.37 r_dihedral_angle_1_deg 7.35 r_long_range_B_refined 5.552 r_scbond_it 5.526 r_mcangle_it 4.717 r_mcbond_it 4.364 r_angle_refined_deg 2.014 r_chiral_restr 0.133 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 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 8352 Nucleic Acid Atoms Solvent Atoms 1105 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing