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Crystal structure of carbonic anhydrase II in complex with a Nir inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CA2 PDB ENTRY 1CA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 100mM Tris.HCl pH 7.7-7.8, 2mM sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.07 α = 90 b = 41.54 β = 104.45 c = 72.39 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 OXFORD SAPPHIRE CCD 2009-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 10.55 94.5 0.11 12.9 3 31515 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 71.1 0.47 2.1 2.1 3156
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 1CA2 2 10.55 15640 822 99.75 0.20236 0.19953 0.2024 0.25725 0.2075 RANDOM 15.861
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 35.829 r_dihedral_angle_4_deg 20.058 r_dihedral_angle_3_deg 17.329 r_dihedral_angle_1_deg 6.22 r_scangle_it 2.218 r_angle_refined_deg 1.516 r_scbond_it 1.374 r_mcangle_it 1.021 r_mcbond_it 0.597 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_4_deg 20.058 r_dihedral_angle_3_deg 17.329 r_dihedral_angle_1_deg 6.22 r_scangle_it 2.218 r_angle_refined_deg 1.516 r_scbond_it 1.374 r_mcangle_it 1.021 r_mcbond_it 0.597 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.249 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.198 r_chiral_restr 0.094 r_metal_ion_refined 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2048 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 58
Software Software Software Name Purpose CrysalisPro data collection AMoRE phasing REFMAC refinement CrysalisPro data reduction SCALEPACK data scaling