7JWN

Crystal structure of Human Serum Albumin in complex with ketoprofen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K2C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7310Prior 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 coefficientSolvent content
2.3848.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.499α = 90
b = 38.878β = 104.47
c = 98.501γ = 90
Symmetry
Space GroupC 1 2 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
12.65096.40.080.0920.0449.34.218925
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)
12.62.6488.50.8030.9250.4470.6121.33.5

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 REPLACEMENTTHROUGHOUT4K2C2.641.921504877280.250.18550.18310.2307RANDOM51.809
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]
0.64-0.22-0.810.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.975
r_dihedral_angle_3_deg14.491
r_dihedral_angle_4_deg14.246
r_dihedral_angle_1_deg5.092
r_angle_refined_deg1.139
r_angle_other_deg1.111
r_chiral_restr0.044
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_refined0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.975
r_dihedral_angle_3_deg14.491
r_dihedral_angle_4_deg14.246
r_dihedral_angle_1_deg5.092
r_angle_refined_deg1.139
r_angle_other_deg1.111
r_chiral_restr0.044
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4639
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms132

Software

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