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Human serum albumin-palladium(II) agent complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 30% PEG 3350, 0.05M PB 7.0, 5% G, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.356 α = 74.89 b = 92.706 β = 89.73 c = 95.345 γ = 79.88
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 EIGER2 S 9M 2023-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.987 SSRF BL02U1
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 2.5 91.96 98.1 0.177 4.1 3.3 42319
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 2.5 2.56 0.177 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 91.96 40171 2130 98.05 0.2531 0.24973 0.2502 0.31619 0.3127 RANDOM 46.276
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] -1.54 -0.26 -0.17 2.82 -1.45 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 18.165 r_long_range_B_refined 7.246 r_long_range_B_other 7.241 r_dihedral_angle_1_deg 6.748 r_mcangle_it 4.244 r_mcangle_other 4.244 r_scangle_other 4.241 r_scbond_it 2.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 18.165 r_long_range_B_refined 7.246 r_long_range_B_other 7.241 r_dihedral_angle_1_deg 6.748 r_mcangle_it 4.244 r_mcangle_other 4.244 r_scangle_other 4.241 r_scbond_it 2.634 r_scbond_other 2.634 r_mcbond_it 2.63 r_mcbond_other 2.629 r_angle_refined_deg 1.527 r_angle_other_deg 1.016 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 8886 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement DIALS data scaling HKL-3000 data reduction PHASER phasing