2QO6

Crystal structure of the glycine 55 arginine mutant of zebrafish liver bile acid-binding protein complexed with cholic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QO4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629820% PEG 4000, 20% isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.652.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.496α = 90
b = 43.496β = 90
c = 67.348γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platetoroidal mirror2005-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.875098.30.0720.0726.63.5110161101625.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9492.10.3270.3271.73.3960

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2QO41.9259964996449593.170.206570.206570.204720.24458RANDOM17.598
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]
0.170.080.17-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.137
r_dihedral_angle_3_deg13.297
r_dihedral_angle_4_deg7.995
r_dihedral_angle_1_deg5.898
r_scangle_it2.31
r_scbond_it1.447
r_angle_refined_deg1.28
r_mcangle_it0.84
r_mcbond_it0.532
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.137
r_dihedral_angle_3_deg13.297
r_dihedral_angle_4_deg7.995
r_dihedral_angle_1_deg5.898
r_scangle_it2.31
r_scbond_it1.447
r_angle_refined_deg1.28
r_mcangle_it0.84
r_mcbond_it0.532
r_nbtor_refined0.307
r_nbd_refined0.18
r_symmetry_vdw_refined0.135
r_symmetry_hbond_refined0.122
r_xyhbond_nbd_refined0.109
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms979
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
AUTOMARdata reduction