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Crystal structure of carbonic anhydrase XIII with 2-(benzylthio)phenyl sulfamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M sodium citrate pH5.5, 0.1M sodium acetate pH4.5 and 26% of PEG4000
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.051 α = 90 b = 57.051 β = 90 c = 159.446 γ = 90
Symmetry Space Group P 43 21 2
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 79.72 100 0.076 0.078 0.015 1 25.1 25.9 52973
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 99.9 2.329 2.376 0.464 0.678 25.6
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 53.72 47559 5310 99.97 0.15775 0.15247 0.1671 0.20717 0.2135 RANDOM 24.352
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] 0.82 0.82 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.303 r_sphericity_free 22.886 r_sphericity_bonded 16.778 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 7.117 r_rigid_bond_restr 7.08 r_long_range_B_refined 4.774 r_scbond_it 4.631 r_mcangle_it 3.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.303 r_sphericity_free 22.886 r_sphericity_bonded 16.778 r_dihedral_angle_4_deg 15.435 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 7.117 r_rigid_bond_restr 7.08 r_long_range_B_refined 4.774 r_scbond_it 4.631 r_mcangle_it 3.846 r_mcbond_it 3.609 r_angle_refined_deg 2.042 r_chiral_restr 0.284 r_bond_refined_d 0.02 r_gen_planes_refined 0.015 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 2068 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction Coot model building MOLREP phasing XDS data reduction