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The X-ray structure of the adduct formed in the reaction between hen egg white lysozyme and arsenoplatin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 20% ethylene glycol, 0.1 M sodium acetate at pH 4.5, 0.6 M sodium nitrate. Crystals of the adduct with AP1 were obtained upon two days soaking of pregrown HEWL crystals in a solution containing 5 mM AP1 dissolved in DMSO and added to the crystal mother liquor.
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.512 α = 90 b = 79.512 β = 90 c = 35.906 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 2014-10-09 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 1.85 56.23 97.7 0.084 24.9 3.2 10091
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 87.6 0.487 2 2
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 4J1A 1.85 56.22 9573 491 97.77 0.18535 0.18239 0.1909 0.24153 0.2438 RANDOM 35.641
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] -2.42 -2.42 4.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_4_deg 21.481 r_dihedral_angle_3_deg 15.434 r_long_range_B_refined 7.415 r_long_range_B_other 7.278 r_dihedral_angle_1_deg 6.897 r_scangle_other 5.765 r_scbond_it 3.975 r_scbond_other 3.88 r_mcangle_other 3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_4_deg 21.481 r_dihedral_angle_3_deg 15.434 r_long_range_B_refined 7.415 r_long_range_B_other 7.278 r_dihedral_angle_1_deg 6.897 r_scangle_other 5.765 r_scbond_it 3.975 r_scbond_other 3.88 r_mcangle_other 3.21 r_mcangle_it 3.209 r_mcbond_it 2.493 r_mcbond_other 2.44 r_angle_refined_deg 1.957 r_angle_other_deg 1.026 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1007 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing