☰ Navigation Tabs
X-ray structure of human serum albumin complexed with cisplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HK1 PDB code 1HK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 Crystals of a cisplatin/HSA adduct were obtained by soaking: more in detail, crystals of defatted HSA, grown after four weeks by sitting drop vapour diffusion method at 25 C using a reservoir solution of 30 % w/v polyethylene glycol 3350 in 50 mM potassium phosphate at pH 7.4 and protein concentration of 30 mg mL-1 (see experimental section or further details), were soaked for 24 h in a 0.005 M cisplatin solution in the same reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.789 α = 90 b = 86.474 β = 103.7 c = 59.141 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 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 3.16 57.46 96.4 0.149 2.5 9393 9393
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-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 PDB code 1HK1 3.16 57.46 8934 449 96.22 0.22781 0.22781 0.22311 0.2223 0.32943 0.3264 RANDOM 49.033
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] 2.23 0.72 -0.98 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 16.433 r_long_range_B_refined 7.722 r_long_range_B_other 7.722 r_dihedral_angle_1_deg 5.907 r_mcangle_it 4.733 r_mcangle_other 4.733 r_scangle_other 4.639 r_mcbond_it 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.947 r_dihedral_angle_4_deg 19.571 r_dihedral_angle_3_deg 16.433 r_long_range_B_refined 7.722 r_long_range_B_other 7.722 r_dihedral_angle_1_deg 5.907 r_mcangle_it 4.733 r_mcangle_other 4.733 r_scangle_other 4.639 r_mcbond_it 2.84 r_mcbond_other 2.833 r_scbond_it 2.81 r_scbond_other 2.81 r_angle_refined_deg 1.384 r_angle_other_deg 0.829 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 4195 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 11
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling