1RJK

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD 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 1DB1PDB entry 1DB1

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
2.0138.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.6α = 90
b = 43.292β = 96.07
c = 41.848γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM R2002-10-27MSINGLE 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
11.9933.07990.05110.84.919031189403
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)
1.992.08960.1613.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1DB11.9930189371893797799.540.188140.188140.185020.24433RANDOM30.927
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]
-2.94-0.483.45-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.895
r_scangle_it4.184
r_scbond_it2.573
r_mcangle_it1.637
r_angle_refined_deg1.394
r_mcbond_it0.87
r_nbd_refined0.206
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.133
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.895
r_scangle_it4.184
r_scbond_it2.573
r_mcangle_it1.637
r_angle_refined_deg1.394
r_mcbond_it0.87
r_nbd_refined0.206
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.133
r_chiral_restr0.089
r_symmetry_hbond_refined0.089
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1990
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
LSCALEdata scaling
MOLREPphasing