2QO4

Crystal structure 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 1TW4PDB ENTRY 1TW4

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
2.6152.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.355α = 90
b = 43.355β = 90
c = 67.526γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315toroidal mirror2005-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.98ESRFID29

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
11.533.894.30.0720.07213.82.8214712147110.6
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)
11.51.5872.60.0830.0836.31.92397

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TW41.5252033820338110494.340.187570.187570.186410.20883RANDOM10.209
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]
-0.1-0.05-0.10.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_3_deg11.245
r_dihedral_angle_4_deg5.542
r_dihedral_angle_1_deg5.488
r_scangle_it2.214
r_scbond_it1.38
r_angle_refined_deg1.183
r_mcangle_it0.782
r_mcbond_it0.494
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_3_deg11.245
r_dihedral_angle_4_deg5.542
r_dihedral_angle_1_deg5.488
r_scangle_it2.214
r_scbond_it1.38
r_angle_refined_deg1.183
r_mcangle_it0.782
r_mcbond_it0.494
r_nbtor_refined0.309
r_nbd_refined0.174
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.084
r_chiral_restr0.073
r_symmetry_hbond_refined0.061
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms972
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing