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Human carbonic anhydrase II in complex with (R)-rosiglitazone
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 2.09 41.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.574 α = 90 b = 41.282 β = 104.416 c = 71.932 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 41.28 99.7 0.064 0.04 0.999 14.6 6.6 59530
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 0.443 0.294 0.865
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 40.165 59512 2935 99.627 0.117 0.1158 0.1158 0.1457 0.1458 12.774
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] -0.253 0.173 -0.439 0.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 21.366 r_dihedral_angle_3_deg 11.457 r_dihedral_angle_1_deg 7.161 r_lrange_it 2.777 r_lrange_other 2.288 r_scangle_it 2.027 r_scangle_other 2.027 r_angle_refined_deg 1.623 r_scbond_it 1.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 21.366 r_dihedral_angle_3_deg 11.457 r_dihedral_angle_1_deg 7.161 r_lrange_it 2.777 r_lrange_other 2.288 r_scangle_it 2.027 r_scangle_other 2.027 r_angle_refined_deg 1.623 r_scbond_it 1.556 r_scbond_other 1.556 r_mcangle_other 1.527 r_mcangle_it 1.525 r_angle_other_deg 1.468 r_rigid_bond_restr 1.156 r_mcbond_other 1.136 r_mcbond_it 1.135 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.197 r_nbd_other 0.197 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.125 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 313 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing