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Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 1.6 M sodium citrate, Tris 50 mM
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.264 α = 90 b = 41.367 β = 104.21 c = 72.276 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 PILATUS 6M 2014-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.000 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.1 29.1 80.7 0.048 0.057 12.9 3.45 78925 -3 15.075
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.17 27.2 0.421 0.554 1.73
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 3P58 1.1 29.1 75094 3814 80.74 0.11 0.109 0.1097 0.1299 0.1308 RANDOM 15.743
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] 0.24 -0.08 -0.15 -0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.448 r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 24.683 r_sphericity_bonded 11.081 r_dihedral_angle_3_deg 10.739 r_dihedral_angle_1_deg 6.406 r_mcangle_it 1.678 r_angle_refined_deg 1.311 r_mcbond_it 1.196 r_mcbond_other 1.195
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.448 r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 24.683 r_sphericity_bonded 11.081 r_dihedral_angle_3_deg 10.739 r_dihedral_angle_1_deg 6.406 r_mcangle_it 1.678 r_angle_refined_deg 1.311 r_mcbond_it 1.196 r_mcbond_other 1.195 r_rigid_bond_restr 1.079 r_angle_other_deg 0.787 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2027 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling MOLREP phasing XSCALE data reduction