9ETD

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528112% wt/vol PEG-3500 and 100 mM sodium formate, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.3848.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.335α = 90
b = 60.631β = 95.9
c = 61.672γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
12.361.341000.0450.0480.018117.771197158.6
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)
12.32.421000.6870.740.2730.8922.4

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 REPLACEMENTTHROUGHOUT2.361.341137558499.990.223650.220430.27956RANDOM62.515
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]
-0.040.020.1-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.597
r_dihedral_angle_3_deg19.935
r_dihedral_angle_4_deg14.582
r_long_range_B_refined12.058
r_mcangle_it8.967
r_dihedral_angle_1_deg7.806
r_scbond_it7.397
r_mcbond_it6.379
r_angle_refined_deg1.586
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.597
r_dihedral_angle_3_deg19.935
r_dihedral_angle_4_deg14.582
r_long_range_B_refined12.058
r_mcangle_it8.967
r_dihedral_angle_1_deg7.806
r_scbond_it7.397
r_mcbond_it6.379
r_angle_refined_deg1.586
r_chiral_restr0.107
r_gen_planes_refined0.008
r_bond_refined_d0.006
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 Atoms1824
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing