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The coumarin-binding site in carbonic anhydrase: the antiepileptic lacosamide as an example
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 Tris.HCl pH 7.7-7.8 , sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.09 41.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.19 α = 90 b = 41.55 β = 104.56 c = 72.23 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 2009-01-15 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 20 0.1 21.2 16806 16696 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 2.05 0.22 4.7 3.8 2087
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 11.88 15674 838 99.89 0.25691 0.25506 0.2526 0.29156 0.3087 RANDOM 9.816
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 35.425 r_dihedral_angle_3_deg 18.955 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_1_deg 7.465 r_scangle_it 3.254 r_scbond_it 2.337 r_angle_refined_deg 1.802 r_mcangle_it 1.386 r_mcbond_it 0.997 r_symmetry_hbond_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.425 r_dihedral_angle_3_deg 18.955 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_1_deg 7.465 r_scangle_it 3.254 r_scbond_it 2.337 r_angle_refined_deg 1.802 r_mcangle_it 1.386 r_mcbond_it 0.997 r_symmetry_hbond_refined 0.327 r_nbtor_refined 0.315 r_nbd_refined 0.271 r_symmetry_vdw_refined 0.266 r_xyhbond_nbd_refined 0.248 r_chiral_restr 0.125 r_metal_ion_refined 0.059 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 2039 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 30
Software Software Software Name Purpose CrysalisPro data collection AMoRE phasing REFMAC refinement CrysalisPro data reduction SCALEPACK data scaling