9ETC

Crystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with chenodeoxycholic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7O0K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5281200 mM sodium chloride, 25 % wt/vol PEG-3500 and 100 mM HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.448.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.564α = 90
b = 60.763β = 99.55
c = 63.546γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95373DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.6562.6799.20.0460.0490.0190.99916.473284630.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.740.8510.9170.340.8762.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6543.6631255158199.180.205360.20260.26189RANDOM38.907
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.321
r_dihedral_angle_3_deg13.835
r_dihedral_angle_4_deg9.973
r_long_range_B_refined7.778
r_dihedral_angle_1_deg7.214
r_mcangle_it4.458
r_scbond_it4.33
r_mcbond_it3.22
r_angle_refined_deg1.568
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.321
r_dihedral_angle_3_deg13.835
r_dihedral_angle_4_deg9.973
r_long_range_B_refined7.778
r_dihedral_angle_1_deg7.214
r_mcangle_it4.458
r_scbond_it4.33
r_mcbond_it3.22
r_angle_refined_deg1.568
r_chiral_restr0.122
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1923
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing