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Human carbonic anhydrase II in complex with pioglitazone
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 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.379 α = 90 b = 41.437 β = 104.38 c = 72.069 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 41.44 99.9 0.062 0.039 0.999 14.8 6.7 59758
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 0.479 0.32 0.862
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 35.658 59740 2937 99.881 0.12 0.1187 0.1185 0.1454 0.1452 13.912
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] -0.558 0.187 -0.374 0.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 7.15 r_lrange_it 2.915 r_lrange_other 2.597 r_scangle_it 2.338 r_scangle_other 2.338 r_scbond_other 1.855 r_scbond_it 1.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 7.15 r_lrange_it 2.915 r_lrange_other 2.597 r_scangle_it 2.338 r_scangle_other 2.338 r_scbond_other 1.855 r_scbond_it 1.854 r_mcangle_other 1.73 r_mcangle_it 1.727 r_angle_refined_deg 1.708 r_angle_other_deg 1.491 r_mcbond_it 1.264 r_mcbond_other 1.26 r_rigid_bond_restr 1.241 r_nbd_refined 0.246 r_symmetry_xyhbond_nbd_refined 0.238 r_xyhbond_nbd_refined 0.236 r_nbd_other 0.2 r_symmetry_nbd_other 0.199 r_symmetry_nbd_refined 0.178 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.126 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.082 r_metal_ion_refined 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing