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Three dimensional structure of human carbonic anhydrase IX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 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 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.67 α = 90 b = 152.67 β = 90 c = 170.7 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 PILATUS 6M 2016-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.87 31.7 99.3 0.052 9.9 2.7 121775 26.8
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 1.87 1.97 99.1 0.476 2 2.7
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 3IAI 1.87 31.7 115490 6280 99.29 0.17337 0.17193 0.1809 0.19894 0.2076 RANDOM 34.494
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] 0.35 0.17 0.35 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.065 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 11.923 r_long_range_B_refined 6.47 r_long_range_B_other 6.263 r_dihedral_angle_1_deg 5.84 r_scangle_other 4.039 r_mcangle_it 3.189 r_mcangle_other 3.188 r_scbond_it 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.065 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 11.923 r_long_range_B_refined 6.47 r_long_range_B_other 6.263 r_dihedral_angle_1_deg 5.84 r_scangle_other 4.039 r_mcangle_it 3.189 r_mcangle_other 3.188 r_scbond_it 2.52 r_scbond_other 2.519 r_mcbond_it 2.036 r_mcbond_other 2.035 r_angle_refined_deg 1.376 r_angle_other_deg 0.901 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7656 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SCALA data scaling