2O4J

Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RJKPDB ENTRY 1RJK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1macroseeding in batch7295PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9838.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.5α = 90
b = 42.4β = 96.5
c = 41.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM RMontel Optics2005-11-30SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.7442.599.80.044819.46.127636275772
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.741.8599.40.3212.863.544160

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1RJK1.74302624126241138898.430.2010.1990.246RANDOM26.413
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]
-2.5-0.432.91-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.045
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg13.933
r_dihedral_angle_1_deg5.027
r_scangle_it3.866
r_scbond_it2.507
r_mcangle_it1.628
r_angle_refined_deg1.56
r_mcbond_it1.022
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.045
r_dihedral_angle_4_deg19.253
r_dihedral_angle_3_deg13.933
r_dihedral_angle_1_deg5.027
r_scangle_it3.866
r_scbond_it2.507
r_mcangle_it1.628
r_angle_refined_deg1.56
r_mcbond_it1.022
r_nbtor_refined0.309
r_nbd_refined0.213
r_symmetry_hbond_refined0.166
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.148
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2000
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
LSCALEdata scaling