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Human carbonic anhydrase II in complex with troglitazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ODZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 Protein concentration was 4 mg/mL; equal volumes (250 nL) of protein plus reservoir were added to the plate; the reservoir was 1.5 M tri-potassium citrate, 0.1 M tris buffer at pH 8.3.
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.333 α = 90 b = 41.292 β = 104.356 c = 71.688 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 9M 2019-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953656 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 41.29 99.1 0.071 0.045 0.998 12.2 6.6 58740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.627 0.416 0.825
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6odz 1.3 39.943 58729 2900 99.112 0.122 0.1204 0.1196 0.151 0.1518 14.036
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] -0.295 -0.669 -1.03 1.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.238 r_dihedral_angle_4_deg 20.433 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_1_deg 7.132 r_lrange_it 2.961 r_lrange_other 2.689 r_scangle_it 2.515 r_scangle_other 2.514 r_rigid_bond_restr 2.063 r_scbond_it 2.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.238 r_dihedral_angle_4_deg 20.433 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_1_deg 7.132 r_lrange_it 2.961 r_lrange_other 2.689 r_scangle_it 2.515 r_scangle_other 2.514 r_rigid_bond_restr 2.063 r_scbond_it 2.017 r_scbond_other 2.013 r_mcangle_other 1.86 r_mcangle_it 1.856 r_angle_refined_deg 1.608 r_angle_other_deg 1.452 r_mcbond_it 1.446 r_mcbond_other 1.446 r_nbd_refined 0.245 r_symmetry_nbd_refined 0.245 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_other 0.21 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.175 r_xyhbond_nbd_other 0.125 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.048 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing