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Crystal structure of human carbonic anhydrase isozyme II with 4-[N-(6-chloro-5-formyl-2-methylthiopyrimidin-4-yl)amino]benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NNO PDB ENTRY 2NNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 0.1M Na-bicine pH 9, 2M Na-malonate pH 7, 0.2M ammonium sulfate , VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.13 α = 90 b = 41.211 β = 104.3 c = 72.076 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 MAR CCD 165 mm Bent, vertically focussing mirror 2007-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
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 1.15 41.211 99.9 0.066 0.066 20.3 6.7 85279 85194 8.522
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) 1.15 1.21 99.7 0.323 0.323 4.1 6.1 12339
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 (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 2NNO 1.15 40.83 85175 85175 8562 99.91 0.177 0.177 0.176 0.1722 0.192 0.1901 RANDOM 11.419
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] 0.16 0.06 -0.31 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.051 r_dihedral_angle_4_deg 19.939 r_dihedral_angle_3_deg 10.577 r_dihedral_angle_1_deg 6.175 r_sphericity_free 2.264 r_sphericity_bonded 2.132 r_scangle_it 2.021 r_scbond_it 1.374 r_angle_refined_deg 1.182 r_mcangle_it 1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.051 r_dihedral_angle_4_deg 19.939 r_dihedral_angle_3_deg 10.577 r_dihedral_angle_1_deg 6.175 r_sphericity_free 2.264 r_sphericity_bonded 2.132 r_scangle_it 2.021 r_scbond_it 1.374 r_angle_refined_deg 1.182 r_mcangle_it 1.066 r_rigid_bond_restr 0.873 r_mcbond_it 0.63 r_nbtor_refined 0.309 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.104 r_symmetry_hbond_refined 0.096 r_metal_ion_refined 0.085 r_chiral_restr 0.082 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection O model building