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X-ray structure of the adduct formed upon treating lysozyme with an aged solution of 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 4 298 20% ethylene glycol
0.1 M sodium acetate pH 4.0
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.86 33.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.703 α = 90 b = 78.703 β = 90 c = 34.462 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 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 2.15 55.65 99.5 0.113 8 5.7 6242
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 2.15 2.19 100 0.639 5.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4J1A 2.153 25.939 6221 289 99.632 0.187 0.1847 0.1919 0.2389 0.2389 32.612
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] -0.658 -0.658 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.613 r_dihedral_angle_4_deg 20.072 r_dihedral_angle_3_deg 17.939 r_dihedral_angle_1_deg 7.917 r_lrange_it 7.114 r_lrange_other 7.112 r_scangle_it 4.249 r_scangle_other 4.247 r_mcangle_it 3.674 r_mcangle_other 3.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.613 r_dihedral_angle_4_deg 20.072 r_dihedral_angle_3_deg 17.939 r_dihedral_angle_1_deg 7.917 r_lrange_it 7.114 r_lrange_other 7.112 r_scangle_it 4.249 r_scangle_other 4.247 r_mcangle_it 3.674 r_mcangle_other 3.672 r_scbond_it 2.724 r_scbond_other 2.722 r_mcbond_other 2.302 r_mcbond_it 2.301 r_angle_refined_deg 1.696 r_angle_other_deg 1.322 r_nbd_other 0.277 r_metal_ion_refined 0.27 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.234 r_symmetry_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.155 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_ext_dist_refined_d 0.063 r_xyhbond_nbd_other 0.053 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing