4QJR

Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to its hormone pip3 at 2.4 a resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YOWPDB entry 1YOW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27710% PEG 8K, 0.025M MGOAC, 30% GLYCEROL, 0.067MM PIP3, 0.80MM 14MER EEPSLLKKLLLAPA, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
3.3262.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.85α = 90
b = 74.85β = 90
c = 139.63γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2013-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.429.16599.60.04324.611.91620516205
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)RedundancyNumber Unique Reflections (All)
12.42.4698.50.710.711.18.91136

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 1YOW2.429.1652.031609980399.520.19140.18950.229676.3499
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
f_dihedral_angle_d20.036
f_angle_d0.589
f_chiral_restr0.04
f_bond_d0.002
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2038
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms75

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing