3VHV

Mineralocorticoid receptor ligand-binding domain with non-steroidal antagonist


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42930.1M HEPES pH 7.4, 0.88M potassium/sodium tartrate, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.612α = 90
b = 62.612β = 90
c = 75.504γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2007-02-17MSINGLE 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
11.355098.60.04522.53.7718631
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)
11.351.488.40.412.22.5

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 2AB21.354068224360898.60.142470.141160.16735RANDOM19.473
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]
-0.29-0.14-0.290.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.043
r_dihedral_angle_3_deg11.852
r_dihedral_angle_4_deg10.561
r_scangle_it7.034
r_scbond_it4.92
r_dihedral_angle_1_deg4.195
r_mcangle_it3.547
r_mcbond_it2.295
r_rigid_bond_restr2.038
r_angle_refined_deg1.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.043
r_dihedral_angle_3_deg11.852
r_dihedral_angle_4_deg10.561
r_scangle_it7.034
r_scbond_it4.92
r_dihedral_angle_1_deg4.195
r_mcangle_it3.547
r_mcbond_it2.295
r_rigid_bond_restr2.038
r_angle_refined_deg1.243
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2084
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms61

Software

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