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Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-chloro-5-formyl-2-methylthiopyrimidin-4-yl)amino]methyl}benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HLJ PDB ENTRY 3HLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Na-bicine pH 9.0, 2M Na-malonate pH 7.55, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.423 α = 90 b = 41.486 β = 104.49 c = 72.434 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 2009-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8120 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 1.7 41.487 100 0.054 0.054 32.8 11.6 27116 27116 13.3
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) 1.7 1.79 100 0.117 0.117 13 7.8 3922
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 PDB ENTRY 3HLJ 1.7 40.1 27090 2727 99.95 0.16752 0.16366 0.1615 0.20202 0.1986 RANDOM 12.678
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] 0.04 -0.09 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.981 r_dihedral_angle_4_deg 21.165 r_dihedral_angle_3_deg 12.803 r_dihedral_angle_1_deg 6.156 r_scangle_it 2.923 r_scbond_it 1.971 r_angle_refined_deg 1.304 r_mcangle_it 1.255 r_mcbond_it 0.773 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.981 r_dihedral_angle_4_deg 21.165 r_dihedral_angle_3_deg 12.803 r_dihedral_angle_1_deg 6.156 r_scangle_it 2.923 r_scbond_it 1.971 r_angle_refined_deg 1.304 r_mcangle_it 1.255 r_mcbond_it 0.773 r_nbtor_refined 0.309 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.092 r_metal_ion_refined 0.049 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection O model building