3ELX

Crystal structure of apo Zebrafish Ileal Bile Acid-Binding Protein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M Sodium HEPES, 1.4 M tri-sodium citrate dihydrate, 1% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.422α = 90
b = 54.422β = 90
c = 82.696γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315toroidal mirror2007-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97ESRFID29

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
11.64199.10.0690.06916.95.2189861898615.8
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)
11.61.691000.2810.2816.45.32731

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 REPLACEMENTTHROUGHOUT2QO41.630189781800197798.660.204330.204330.202460.2398RANDOM17.547
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]
0.360.180.36-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.14
r_dihedral_angle_3_deg14.941
r_dihedral_angle_4_deg13.374
r_dihedral_angle_1_deg5.381
r_scangle_it3.253
r_scbond_it2.088
r_mcangle_it1.274
r_angle_refined_deg1.155
r_mcbond_it0.855
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.14
r_dihedral_angle_3_deg14.941
r_dihedral_angle_4_deg13.374
r_dihedral_angle_1_deg5.381
r_scangle_it3.253
r_scbond_it2.088
r_mcangle_it1.274
r_angle_refined_deg1.155
r_mcbond_it0.855
r_nbtor_refined0.303
r_nbd_refined0.187
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.12
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1030
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling