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Crystal structure of Human Serum Albumin in complex with ketoprofen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K2C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 310 Prior to crystallization, the protein at concentration of 162 mg/ml (dissolved in 50 mM Tris pH 7.4 and 20 mM NaCl) was mixed with 100 mM ketoprofen in 100% DMSO in ratio 9:1 (final ketoprofen concentration 10 mM) and incubated for several hours at 37 oC. Then, 0.2 ul of the protein solution was mixed with 0.2 ul of the well condition (24% PEG 3350, 50 mM K2HPO4 at pH 7.0). The crystallization plate was incubated at RT for 3 months, then for several days at 37 oC, and after the growth of the first HSA crystals, the plate was transferred to RT.
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.499 α = 90 b = 38.878 β = 104.47 c = 98.501 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 6M 2020-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 50 96.4 0.08 0.092 0.044 9.3 4.2 18925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 88.5 0.803 0.925 0.447 0.612 1.3 3.5
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 4K2C 2.6 41.92 15048 772 80.25 0.1855 0.1831 0.1918 0.2307 0.2441 RANDOM 51.809
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] 0.64 -0.22 -0.81 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.975 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.139 r_angle_other_deg 1.111 r_chiral_restr 0.044 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.975 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_4_deg 14.246 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.139 r_angle_other_deg 1.111 r_chiral_restr 0.044 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4639 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 132
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot model building