3UP0 | pdb_00003up0

Nuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in complex with (25S)-delta7-dafachronic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SITTING DROP	5.1	293	26% w/v PEG2000, 0.2 M ammonium acetate, pH 5.1, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.012	α = 90
b = 85.163	β = 107.1
c = 66.127	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		2009-03-10	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	1.597	45.89				67287	67280	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.597	1.66	100		0.609

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	1.6	45.89	67287	66973	4855	99.99	0.1848	0.1848	0.1834	0.19	0.2019	0.21	RANDOM	19.3318

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]
0.05		0.15	-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.603
r_dihedral_angle_4_deg	19.291
r_dihedral_angle_3_deg	11.042
r_scangle_it	4.884
r_dihedral_angle_1_deg	4.08
r_scbond_it	2.973
r_mcangle_it	1.953
r_angle_refined_deg	1.363
r_mcbond_it	1.035
r_angle_other_deg	0.893

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.603
r_dihedral_angle_4_deg	19.291
r_dihedral_angle_3_deg	11.042
r_scangle_it	4.884
r_dihedral_angle_1_deg	4.08
r_scbond_it	2.973
r_mcangle_it	1.953
r_angle_refined_deg	1.363
r_mcbond_it	1.035
r_angle_other_deg	0.893
r_mcbond_other	0.251
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4093
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	60

Software

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

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.