3EM0

Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form B).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M Sodium HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.0269.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.285α = 90
b = 85.285β = 127.65
c = 75.055γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmDouble crystal (Si111, Si220)2006-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.03ELETTRA5.2R

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
12.23098.60.0590.0599.13.1241252412543.6
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)
12.22.3297.30.3120.3121.33.12395

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 REPLACEMENTTHROUGHOUT3ELZ2.2302412522888123798.630.22720.22720.225660.25422RANDOM38.977
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]
0.370.340.53-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.923
r_dihedral_angle_4_deg23.375
r_dihedral_angle_3_deg17.106
r_dihedral_angle_1_deg5.476
r_scangle_it2.16
r_angle_refined_deg1.536
r_scbond_it1.414
r_mcangle_it1.003
r_mcbond_it0.589
r_nbtor_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.923
r_dihedral_angle_4_deg23.375
r_dihedral_angle_3_deg17.106
r_dihedral_angle_1_deg5.476
r_scangle_it2.16
r_angle_refined_deg1.536
r_scbond_it1.414
r_mcangle_it1.003
r_mcbond_it0.589
r_nbtor_refined0.33
r_nbd_refined0.202
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.114
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2055
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms261

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction