7C7V

Vitamin D3 receptor/lithochoric acid derivative complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZLC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
1.7830.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.045α = 90
b = 36.898β = 96.963
c = 39.486γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS 6M2015-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
124097.40.0940.9967.13.315052
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.130.630.911.63

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2ZLC2401503676297.3390.2010.19770.267844.663
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]
-5.813-0.9313.6882.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.53
r_dihedral_angle_3_deg16.167
r_dihedral_angle_4_deg14.415
r_lrange_it8.286
r_lrange_other8.284
r_scangle_it6.577
r_scangle_other6.575
r_dihedral_angle_1_deg6.291
r_mcangle_it5.054
r_mcangle_other5.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.53
r_dihedral_angle_3_deg16.167
r_dihedral_angle_4_deg14.415
r_lrange_it8.286
r_lrange_other8.284
r_scangle_it6.577
r_scangle_other6.575
r_dihedral_angle_1_deg6.291
r_mcangle_it5.054
r_mcangle_other5.052
r_scbond_it4.439
r_scbond_other4.436
r_mcbond_it3.543
r_mcbond_other3.542
r_angle_refined_deg1.578
r_angle_other_deg1.333
r_nbd_other0.246
r_nbd_refined0.212
r_symmetry_nbd_other0.194
r_symmetry_nbd_refined0.162
r_nbtor_refined0.161
r_xyhbond_nbd_refined0.142
r_symmetry_nbtor_other0.083
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_symmetry_xyhbond_nbd_other0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1959
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing