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X-ray structure of the protein-gold adduct formed upon reaction of Aubipic with hen egg white lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A PDB code 4J1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 crystal of lysozyme have been obtained in the presence of Aubipyc (1:10 protein to metal ratio) via the hanging drop vapor diffusion method. These crystals have been grown using a reservoir solution of 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.979 α = 90 b = 76.979 β = 90 c = 38.089 γ = 90
Symmetry Space Group P 43 21 2
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 RIGAKU SATURN 944+ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 94.7 0.048 3 10554 10554
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 FOURIER SYNTHESIS THROUGHOUT PDB code 4J1A 1.8 25.55 9988 499 94.44 0.18383 0.18075 0.1895 0.24378 0.2466 RANDOM 30.89
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] -0.75 -0.75 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.141 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_4_deg 13.567 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 5.987 r_long_range_B_other 5.849 r_scangle_other 4.216 r_mcangle_other 3.121 r_mcangle_it 3.12 r_scbond_it 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.141 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_4_deg 13.567 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 5.987 r_long_range_B_other 5.849 r_scangle_other 4.216 r_mcangle_other 3.121 r_mcangle_it 3.12 r_scbond_it 3.099 r_scbond_other 2.946 r_mcbond_it 2.412 r_mcbond_other 2.402 r_angle_refined_deg 1.671 r_angle_other_deg 0.967 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing