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)
Type	Source	Accession Code	Details
experimental model	PDB	3ELZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M Sodium HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.37

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm	Double crystal (Si111, Si220)	2006-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.03	ELETTRA	5.2R

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	30	98.6	0.059	0.059	9.1	3.1	24125	24125			43.6

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)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	97.3		0.312	0.312	1.3	3.1	2395

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ELZ	2.2	30	24125	22888	1237	98.63	0.2272	0.2272	0.22566	0.25422	RANDOM	38.977

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]
0.37		0.34	0.53		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.923
r_dihedral_angle_4_deg	23.375
r_dihedral_angle_3_deg	17.106
r_dihedral_angle_1_deg	5.476
r_scangle_it	2.16
r_angle_refined_deg	1.536
r_scbond_it	1.414
r_mcangle_it	1.003
r_mcbond_it	0.589
r_nbtor_refined	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.923
r_dihedral_angle_4_deg	23.375
r_dihedral_angle_3_deg	17.106
r_dihedral_angle_1_deg	5.476
r_scangle_it	2.16
r_angle_refined_deg	1.536
r_scbond_it	1.414
r_mcangle_it	1.003
r_mcbond_it	0.589
r_nbtor_refined	0.33
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.158
r_symmetry_hbond_refined	0.12
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2055
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	261

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.