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Crystal structure of 1-hydroxy-5-methylpyridine-2(1H)-thione bound to human carbonic anhydrase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KS3 PDB entry 3KS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 291 Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.062 α = 90 b = 41.168 β = 104.35 c = 71.577 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 CCD BRUKER SMART 6000 2014-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5478
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 35.4 99.33 29998 29793 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.641 97.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3KS3 1.6 35.4 1 29998 29793 1580 99.33 0.17 0.16945 0.16728 0.1673 0.21171 0.2109 RANDOM 11.924
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 r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 22.847 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.892 r_scangle_it 5.32 r_scbond_it 3.405 r_mcangle_it 2.375 r_angle_refined_deg 2.13 r_mcbond_it 1.425 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.529 r_dihedral_angle_4_deg 22.847 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.892 r_scangle_it 5.32 r_scbond_it 3.405 r_mcangle_it 2.375 r_angle_refined_deg 2.13 r_mcbond_it 1.425 r_chiral_restr 0.163 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 24
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement APEX data reduction