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Crystal structure of Human Serum Albumin complex with JMS-053
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 311 Prior to crystallization, protein was incubated with myristic acid (5 mM final concentration of fatty acid) for several hours at 37 oC. Then, 0.2 ul of 100 mg/ml protein in 25 mM Tris (pH 7.4) and 50 mM NaCl were mixed with 0.2 ul of the well condition (25% PEG 3350, 50 mM K2HPO4 at pH 7.0), the crystallization plate was incubated at 37oC for several days and, after growth of the first HSA crystals, the plate was transferred to RT. JMS-053 powder (~50 ug) was added to the crystallization drop containing crystals, and then incubated for 48 h before harvesting.
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.443 α = 74.63 b = 93.44 β = 89.63 c = 94.908 γ = 80.44
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 2.2 50 92.9 0.05 0.063 0.038 10.4 2.6 59720
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 2.2 2.24 91 0.678 0.862 0.525 0.609 2.5
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 6HSC 2.2 46.01 51130 2640 84.33 0.195 0.1924 0.198 0.2469 0.2474 RANDOM 44.29
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] -0.34 0.28 0.35 0.74 -0.2 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.797 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 14.543 r_dihedral_angle_1_deg 5.046 r_angle_other_deg 1.432 r_angle_refined_deg 1.143 r_chiral_restr 0.048 r_bond_other_d 0.018 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.797 r_dihedral_angle_4_deg 19.003 r_dihedral_angle_3_deg 14.543 r_dihedral_angle_1_deg 5.046 r_angle_other_deg 1.432 r_angle_refined_deg 1.143 r_chiral_restr 0.048 r_bond_other_d 0.018 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9256 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot model building HKL-3000 data scaling