5DBY

Crystal Structure of Equine Serum Albumin in Complex with Diclofenac and Naproxen Obtained in Displacement Experiment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OT2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52932.0 M ammonium sulfate, 0.1 M acetate buffer pH 5.0, unliganded crystal was soaked in the diclofenac solution for 1h and transferred to the naproxen solution for 1h
Crystal Properties
Matthews coefficientSolvent content
2.7755.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.32α = 90
b = 94.32β = 90
c = 141.69γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2015-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
12.355099.90.07715.375.092971629700-3
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)
12.352.451000.9892.035.1

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 REPLACEMENTTHROUGHOUT4OT22.3550.0128576112199.930.194990.193320.23397RANDOM58.944
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]
-0.39-0.19-0.391.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.852
r_dihedral_angle_3_deg18.672
r_dihedral_angle_4_deg17.336
r_dihedral_angle_1_deg6.911
r_long_range_B_refined5.806
r_long_range_B_other5.804
r_angle_refined_deg1.93
r_scangle_other1.463
r_angle_other_deg1.135
r_scbond_it1.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.852
r_dihedral_angle_3_deg18.672
r_dihedral_angle_4_deg17.336
r_dihedral_angle_1_deg6.911
r_long_range_B_refined5.806
r_long_range_B_other5.804
r_angle_refined_deg1.93
r_scangle_other1.463
r_angle_other_deg1.135
r_scbond_it1.045
r_scbond_other1.045
r_mcangle_it0.897
r_mcangle_other0.897
r_mcbond_it0.602
r_mcbond_other0.602
r_chiral_restr0.108
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.003
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 Atoms84
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
REFMACphasing
XSCALEdata scaling
XDSdata reduction