6U4X

Crystal structure of Equine Serum Albumin complex with ibuprofen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V0V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2891 ul of 36 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.4 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Ibuprofen powder was added to the crystallization drop.
Crystal Properties
Matthews coefficientSolvent content
2.8456.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.232α = 90
b = 95.232β = 90
c = 141.939γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.255099.70.1110.1160.0350.996910.734270-3
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)
12.252.29971.1171.2020.4270.6751.136.6

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 REPLACEMENTTHROUGHOUT5v0v2.2547.6627866150785.30.19340.1910.2376RANDOM43.97
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]
0.120.060.12-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.157
r_dihedral_angle_4_deg14.484
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg5.103
r_angle_refined_deg1.148
r_angle_other_deg1.139
r_chiral_restr0.048
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.157
r_dihedral_angle_4_deg14.484
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg5.103
r_angle_refined_deg1.148
r_angle_other_deg1.139
r_chiral_restr0.048
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4568
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms100

Software

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