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Crystal structure of carbonic anhydrase XII with 3-(benzylsulfonyl)phenyl sulfamate
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 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.683 α = 90 b = 74.335 β = 108.65 c = 91.797 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 16M 2024-12-02 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 1.4 86.98 99.2 0.069 0.074 0.028 0.998 11.9 7 192769
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 1.4 1.42 99.2 1.465 1.584 0.595 0.587 6.9
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 1.4 43.53 173661 19033 99.12 0.16897 0.16512 0.1743 0.2044 0.2075 RANDOM 25.463
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] -1.47 -0.58 2.68 -0.66
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.308 r_dihedral_angle_3_deg 12.895 r_mcangle_it 11.526 r_scbond_it 10.219 r_mcbond_it 8.52 r_dihedral_angle_1_deg 7.002 r_dihedral_angle_2_deg 5.791 r_rigid_bond_restr 5.712 r_angle_refined_deg 1.783 r_chiral_restr 0.2
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.308 r_dihedral_angle_3_deg 12.895 r_mcangle_it 11.526 r_scbond_it 10.219 r_mcbond_it 8.52 r_dihedral_angle_1_deg 7.002 r_dihedral_angle_2_deg 5.791 r_rigid_bond_restr 5.712 r_angle_refined_deg 1.783 r_chiral_restr 0.2 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8339 Nucleic Acid Atoms Solvent Atoms 678 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing