4PF3

Mineralocorticoid receptor ligand-binding domain with compuond 37a


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WFG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris pH 8.0, 23% ethanol
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.05α = 90
b = 66.365β = 90
c = 74.908γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

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
11.15095.10.05212.34.6111992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1473.60.3772.12.1

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 REPLACEMENTTHROUGHOUT3WFG1.140106388558295.090.154960.153820.17683RANDOM18.169
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]
0.13-0.20.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.52
r_sphericity_free32.148
r_dihedral_angle_4_deg14.714
r_sphericity_bonded13.599
r_dihedral_angle_3_deg11.27
r_dihedral_angle_1_deg4.91
r_long_range_B_refined4.031
r_scbond_it4.026
r_rigid_bond_restr3.064
r_mcangle_it1.623
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.52
r_sphericity_free32.148
r_dihedral_angle_4_deg14.714
r_sphericity_bonded13.599
r_dihedral_angle_3_deg11.27
r_dihedral_angle_1_deg4.91
r_long_range_B_refined4.031
r_scbond_it4.026
r_rigid_bond_restr3.064
r_mcangle_it1.623
r_angle_refined_deg1.379
r_mcbond_it1.295
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2040
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement