6CI6

Crystal structure of equine serum albumin in complex with nabumetone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V08 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42891 ul of 34 mg/ml protein in 10 mM Tris pH 7.4 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.2 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 10 mM nabumetone
Crystal Properties
Matthews coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.879α = 90
b = 93.879β = 90
c = 140.787γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M1000 um thick sensor. Mirrors: adjustable focus K-B pair Si plus Pt, Rh coatings2016-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97949APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.850.011000.1150.1150.1290.0574.65.117321-363.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.851000.660.660.7420.3350.8164.9

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 REPLACEMENTTHROUGHOUT3V082.850.011649678899.750.18580.18240.2557RANDOM64.159
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]
1.690.841.69-5.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.826
r_dihedral_angle_4_deg15.27
r_dihedral_angle_3_deg13.869
r_dihedral_angle_1_deg4.837
r_angle_refined_deg1.088
r_angle_other_deg0.861
r_chiral_restr0.055
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.826
r_dihedral_angle_4_deg15.27
r_dihedral_angle_3_deg13.869
r_dihedral_angle_1_deg4.837
r_angle_refined_deg1.088
r_angle_other_deg0.861
r_chiral_restr0.055
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4524
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling