5ID7

Crystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cPA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A73 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529328% PEG3350, 50 mM phosphate buffer
Crystal Properties
Matthews coefficientSolvent content
2.244.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.895α = 105.46
b = 85.167β = 89.78
c = 96.308γ = 101.34
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252014-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.2646.3593.50.0512.4249652-344.88
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.490.10.3692.3

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 REPLACEMENTTHROUGHOUT3A732.2645.948640101293.580.207340.20640.25262RANDOM46.163
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]
0.310.60.061.350.79-2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.142
r_dihedral_angle_4_deg24.734
r_dihedral_angle_3_deg18.34
r_long_range_B_refined7.482
r_long_range_B_other7.477
r_dihedral_angle_1_deg6.378
r_scangle_other5.013
r_mcangle_it4.336
r_mcangle_other4.336
r_scbond_it3.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.142
r_dihedral_angle_4_deg24.734
r_dihedral_angle_3_deg18.34
r_long_range_B_refined7.482
r_long_range_B_other7.477
r_dihedral_angle_1_deg6.378
r_scangle_other5.013
r_mcangle_it4.336
r_mcangle_other4.336
r_scbond_it3.233
r_scbond_other3.232
r_mcbond_other2.855
r_mcbond_it2.854
r_angle_refined_deg1.942
r_angle_other_deg1.267
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.007
r_gen_planes_other0.006
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 AtomsNumber
Protein Atoms9260
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms195

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling