1RKH

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing 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
1VAPOR DIFFUSION, HANGING DROP7295PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9737.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.8α = 90
b = 42.291β = 96.15
c = 41.788γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM R2003-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
12.2840.78900.04514.13.712524112853
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)
2.282.38700.1494.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1RJK2.2830112781127855490.110.181870.181870.180020.21764RANDOM29.616
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]
-3.4-0.583.68-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.528
r_scangle_it4.124
r_scbond_it2.512
r_mcangle_it1.465
r_angle_refined_deg1.46
r_mcbond_it0.758
r_nbd_refined0.213
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.129
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.528
r_scangle_it4.124
r_scbond_it2.512
r_mcangle_it1.465
r_angle_refined_deg1.46
r_mcbond_it0.758
r_nbd_refined0.213
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.129
r_chiral_restr0.093
r_bond_refined_d0.016
r_symmetry_hbond_refined0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1994
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
LSCALEdata scaling