3VHU

Mineralocorticoid receptor ligand-binding domain with spironolactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AB2PDB ENTRY 2AB2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES pH 7.0, 1.26M Lithium sulfate, 6% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.526α = 90
b = 171.509β = 90
c = 42.358γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2005-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.000ALS5.0.3

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
12.115098.60.05926.26193661
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)
12.112.290.30.5152.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2AB22.11401829998797.760.193150.190340.24571RANDOM52.646
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]
4.62-2.96-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg15.993
r_dihedral_angle_3_deg15.268
r_scangle_it7.682
r_scbond_it5.262
r_dihedral_angle_1_deg4.835
r_mcangle_it3.185
r_mcbond_it1.923
r_angle_refined_deg1.207
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg15.993
r_dihedral_angle_3_deg15.268
r_scangle_it7.682
r_scbond_it5.262
r_dihedral_angle_1_deg4.835
r_mcangle_it3.185
r_mcbond_it1.923
r_angle_refined_deg1.207
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2034
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms29

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling