5B41

Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293MOPS-Na, Na-formate, PEG 4000, Ethyleneglycol
Crystal Properties
Matthews coefficientSolvent content
2.0840.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.17α = 90
b = 41.75β = 96.02
c = 41.77γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102014-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8935.0295.411.23.120404
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ZLC1.8935.021944595994.960.189430.187120.23443RANDOM37.724
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]
-3.42-0.713.120.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.591
r_dihedral_angle_3_deg17.67
r_dihedral_angle_4_deg15.985
r_long_range_B_other9.836
r_long_range_B_refined9.805
r_scangle_other6.991
r_mcangle_it5.394
r_mcangle_other5.391
r_dihedral_angle_1_deg5.25
r_scbond_it4.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.591
r_dihedral_angle_3_deg17.67
r_dihedral_angle_4_deg15.985
r_long_range_B_other9.836
r_long_range_B_refined9.805
r_scangle_other6.991
r_mcangle_it5.394
r_mcangle_other5.391
r_dihedral_angle_1_deg5.25
r_scbond_it4.5
r_scbond_other4.498
r_mcbond_other3.705
r_mcbond_it3.704
r_angle_refined_deg1.679
r_angle_other_deg0.923
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2005
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement