5ID9

Crystal structure of equine 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 4OT2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52931.8 M Ammonium sulfate, 0.1 M acetate buffer pH 4.5, cocrystallization
Crystal Properties
Matthews coefficientSolvent content
2.7555.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.86α = 90
b = 93.86β = 90
c = 141.79γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-04-12MSINGLE 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)CC (Half)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
12.485099.60.0880.99814.54.624973-353.1
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)
12.482.5899.40.9912.14.7

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 REPLACEMENTTHROUGHOUT4OT22.485023957101299.60.172610.170310.22906RANDOM55.701
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]
0.60.30.6-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.65
r_dihedral_angle_3_deg18.395
r_dihedral_angle_4_deg17.671
r_long_range_B_refined8.1
r_long_range_B_other8.096
r_dihedral_angle_1_deg6.402
r_scangle_other4.929
r_mcangle_it3.719
r_mcangle_other3.719
r_scbond_it2.999
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.65
r_dihedral_angle_3_deg18.395
r_dihedral_angle_4_deg17.671
r_long_range_B_refined8.1
r_long_range_B_other8.096
r_dihedral_angle_1_deg6.402
r_scangle_other4.929
r_mcangle_it3.719
r_mcangle_other3.719
r_scbond_it2.999
r_scbond_other2.987
r_mcbond_other2.318
r_mcbond_it2.317
r_angle_refined_deg1.847
r_angle_other_deg1.038
r_chiral_restr0.11
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4568
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
REFMACphasing
XDSdata reduction
XSCALEdata scaling