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Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4-methyl-6-oxo-1,6-dihydro-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 298 Na-Bicine 0.1M pH 9, Na-Malonate 2.2M pH 7, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.208 α = 90 b = 41.18 β = 104.29 c = 71.918 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 MARMosaic, 225 mm Detector swing-out angle up to 30 degrees 2010-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9748 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.3 41.18 95.9 0.064 0.064 26.2 7.6 56499 12.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 93.6 0.38 0.38 2 7.7 8022
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 3HLJ 1.3 39.84 56499 56478 5694 95.53 0.146 0.142 0.179 0.1764 RANDOM 16.21
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] -0.56 0.54 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 22.139 r_sphericity_free 15.581 r_dihedral_angle_3_deg 12.968 r_sphericity_bonded 9.391 r_dihedral_angle_1_deg 6.606 r_scangle_it 6.284 r_scbond_it 4.992 r_mcangle_it 3.836 r_rigid_bond_restr 3.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 22.139 r_sphericity_free 15.581 r_dihedral_angle_3_deg 12.968 r_sphericity_bonded 9.391 r_dihedral_angle_1_deg 6.606 r_scangle_it 6.284 r_scbond_it 4.992 r_mcangle_it 3.836 r_rigid_bond_restr 3.305 r_mcbond_it 2.928 r_angle_refined_deg 2.348 r_nbtor_refined 0.322 r_nbd_refined 0.226 r_chiral_restr 0.191 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.083 r_bond_refined_d 0.028 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection