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The crystal structure of a NAMI A-Carbonic Anhydrase II adduct discloses the mode of action of this novel anticancer metallodrug
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 41.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.1 α = 90 b = 41.55 β = 104.51 c = 72.29 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 2009-09-20 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 1.8 10.9 83 0.17 15.7 2.9 42492 35616 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) 1.8 1.84 0.41 2.38 1.8 7082
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 1.8 10.87 21463 1100 100 0.19512 0.19307 0.1943 0.23549 0.1938 RANDOM 13.283
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] -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.715 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 5.8 r_scangle_it 2.099 r_scbond_it 1.294 r_angle_refined_deg 1.162 r_mcangle_it 0.89 r_mcbond_it 0.509 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.715 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 15.618 r_dihedral_angle_1_deg 5.8 r_scangle_it 2.099 r_scbond_it 1.294 r_angle_refined_deg 1.162 r_mcangle_it 0.89 r_mcbond_it 0.509 r_nbtor_refined 0.306 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.081 r_metal_ion_refined 0.039 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2048 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 21
Software Software Software Name Purpose CrysalisPro data collection AMoRE phasing REFMAC refinement CrysalisPro data reduction SCALEPACK data scaling