3UP3 | pdb_00003up3

Nuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in complex with (25S)-cholestenoic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			293	20% w/v PEG3350, 0.2 M diammonium tartrate, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.545	α = 90
b = 85.296	β = 106.87
c = 46.325	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2010-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.25	29.295	92.7			70792	64363	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.29	57.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.25	29.29	64400	64363	4660	91.19	0.1672	0.1672	0.1662	0.18	0.1804	0.19	RANDOM	12.5833

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]
0.12		0.08	0.14		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	13.125
r_dihedral_angle_3_deg	11.325
r_dihedral_angle_1_deg	4.914
r_scangle_it	3.918
r_scbond_it	2.464
r_mcangle_it	1.612
r_angle_refined_deg	1.522
r_angle_other_deg	0.907
r_mcbond_it	0.887

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	13.125
r_dihedral_angle_3_deg	11.325
r_dihedral_angle_1_deg	4.914
r_scangle_it	3.918
r_scbond_it	2.464
r_mcangle_it	1.612
r_angle_refined_deg	1.522
r_angle_other_deg	0.907
r_mcbond_it	0.887
r_mcbond_other	0.24
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2048
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	54

Software

Software
Software Name	Purpose
DENZO	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SCALEPACK	data scaling

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.