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Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE)
Crystal Properties Matthews coefficient Solvent content 3.46 64.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.64 α = 90 b = 152.64 β = 90 c = 172.84 γ = 120
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 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97776 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 76.32 100 0.145 6.2 5.2 109432 36.116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 100 0.581 2.6 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6FE2 1.95 76.32 103914 5517 100 0.21481 0.21278 0.2196 0.25328 0.2587 RANDOM 38.237
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.763 r_dihedral_angle_4_deg 19.646 r_dihedral_angle_3_deg 15.464 r_long_range_B_refined 7.982 r_long_range_B_other 7.959 r_dihedral_angle_1_deg 7.381 r_scangle_other 5.879 r_mcangle_it 4.801 r_mcangle_other 4.8 r_scbond_it 3.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.763 r_dihedral_angle_4_deg 19.646 r_dihedral_angle_3_deg 15.464 r_long_range_B_refined 7.982 r_long_range_B_other 7.959 r_dihedral_angle_1_deg 7.381 r_scangle_other 5.879 r_mcangle_it 4.801 r_mcangle_other 4.8 r_scbond_it 3.901 r_scbond_other 3.9 r_mcbond_it 3.295 r_mcbond_other 3.295 r_angle_refined_deg 1.712 r_angle_other_deg 1.378 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7729 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement SCALA data scaling