X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HSC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP311Prior 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 coefficientSolvent content
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.443α = 74.63
b = 93.44β = 89.63
c = 94.908γ = 80.44
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25092.90.050.0630.03810.42.659720
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)RedundancyNumber Unique Reflections (All)
12.22.24910.6780.8620.5250.6092.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6HSC2.246.0151130264084.330.1950.19240.2469RANDOM44.29
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]
-0.340.280.350.74-0.2-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.797
r_dihedral_angle_4_deg19.003
r_dihedral_angle_3_deg14.543
r_dihedral_angle_1_deg5.046
r_angle_other_deg1.432
r_angle_refined_deg1.143
r_chiral_restr0.048
r_bond_other_d0.018
r_bond_refined_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.797
r_dihedral_angle_4_deg19.003
r_dihedral_angle_3_deg14.543
r_dihedral_angle_1_deg5.046
r_angle_other_deg1.432
r_angle_refined_deg1.143
r_chiral_restr0.048
r_bond_other_d0.018
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9256
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms255

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
HKL-3000data scaling