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Room temperature structure of carbonic anhydrase II in complex with vorinostat (drug soak)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ILI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 50 mM Tris HCl pH 8.0,
1.25 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.925 α = 90 b = 41.771 β = 104.499 c = 72.877 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 293 PIXEL DECTRIS EIGER2 X CdTe 16M 2024-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7293 MAX IV BioMAX
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 1.4 25.62 97.9 0.069 0.044 0.995 11.5 3.4 49479 13.15
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 1.4 1.45 85.9 0.411 0.289 0.77 3.4 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 24.08 1.38 48415 3533 89.92 0.1535 0.1525 0.1529 0.1764 0.1756 20.17
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4993 f_angle_d 0.9583 f_chiral_restr 0.087 f_plane_restr 0.0079 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2048 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing