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Crystal structure of carbonic anhydrase XII with methyl 2,4-dichloro-5-(sulfamoyloxy)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 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.727 α = 90 b = 74.632 β = 105.36 c = 76.673 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 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 1.35 74.63 98.6 0.049 0.068 0.036 0.998 9.6 3.4 107327
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 1.35 1.42 97.3 0.373 0.542 0.299 0.806 3.1
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 1.35 52.52 96595 10600 98.5 0.15496 0.15135 0.1605 0.18728 0.1897 RANDOM 19.766
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] -0.58 0.28 -0.6 0.89
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.91 r_dihedral_angle_2_deg 12.242 r_dihedral_angle_3_deg 12.208 r_mcangle_it 7.366 r_scbond_it 7.205 r_dihedral_angle_1_deg 6.848 r_mcbond_it 5.207 r_rigid_bond_restr 5.015 r_angle_refined_deg 1.834 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.91 r_dihedral_angle_2_deg 12.242 r_dihedral_angle_3_deg 12.208 r_mcangle_it 7.366 r_scbond_it 7.205 r_dihedral_angle_1_deg 6.848 r_mcbond_it 5.207 r_rigid_bond_restr 5.015 r_angle_refined_deg 1.834 r_chiral_restr 0.112 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 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 4195 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing