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X-RAY STRUCTURE OF THE ADDUCT BETWEEN HEN EGG WHITE LYSOZYME AND CISPLATIN AT LONG INCUBATION TIMES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Crystals were grown using a reservoir solution of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4 and a drop of 1 uL adduct solution and 1 uL reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.28 α = 90 b = 79.28 β = 90 c = 37.45 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 PIXEL DECTRIS PILATUS 2M 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0650 ELETTRA 5.2R
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 1.55 56.06 97.6 0.095 11.9 5.7 18069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 99.1 1.005 0.273 0.8 5.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 193L 1.55 56.06 16465 868 96.95 0.17005 0.16787 0.21289 0.1934 RANDOM 24.018
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_4_deg 22.43 r_dihedral_angle_3_deg 12.405 r_long_range_B_refined 7.576 r_long_range_B_other 7.268 r_dihedral_angle_1_deg 6.275 r_scangle_other 5.788 r_scbond_it 3.873 r_scbond_other 3.793 r_mcangle_other 2.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_4_deg 22.43 r_dihedral_angle_3_deg 12.405 r_long_range_B_refined 7.576 r_long_range_B_other 7.268 r_dihedral_angle_1_deg 6.275 r_scangle_other 5.788 r_scbond_it 3.873 r_scbond_other 3.793 r_mcangle_other 2.995 r_mcangle_it 2.991 r_mcbond_it 2.122 r_mcbond_other 2.102 r_angle_refined_deg 1.98 r_angle_other_deg 1.206 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 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 1001 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing