☰ Navigation Tabs
Crystal structure of human carbonic anhydrase isozyme II with 5-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide
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 291 Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate and 2M sodium malonate, pH 7.0 made from 1M sodium BICINE and 3.4M sodium malonate, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.233 α = 90 b = 41.112 β = 104.05 c = 72.109 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 2009-12-21 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 1.5 39.81 98 0.045 0.045 35.9 9.9 37890
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) 1.5 1.58 97.1 0.324 0.324 6 9.9
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3HLJ 1.5 39.81 38726 34084 3806 97.84 0.13976 0.13479 0.184 0.1735 RANDOM 16.463
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] -0.06 0.04 -0.03 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.237 r_dihedral_angle_4_deg 23.93 r_sphericity_free 13.164 r_dihedral_angle_3_deg 12.66 r_sphericity_bonded 7.872 r_scangle_it 6.55 r_dihedral_angle_1_deg 6.344 r_scbond_it 4.887 r_mcangle_it 3.685 r_rigid_bond_restr 3.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.237 r_dihedral_angle_4_deg 23.93 r_sphericity_free 13.164 r_dihedral_angle_3_deg 12.66 r_sphericity_bonded 7.872 r_scangle_it 6.55 r_dihedral_angle_1_deg 6.344 r_scbond_it 4.887 r_mcangle_it 3.685 r_rigid_bond_restr 3.029 r_mcbond_it 2.819 r_angle_refined_deg 2.224 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.299 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.219 r_chiral_restr 0.192 r_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.054 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection