1QKM

HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EREPDB ENTRY 1ERE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.16-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1
Crystal Properties
Matthews coefficientSolvent content
2.4449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.12α = 90
b = 63.12β = 90
c = 250.23γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1998-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.86099.70.04915828523-332.6
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)
11.81.831000.43348

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ERE1.85528460144199.70.2150.252RANDOM41.3
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]
3.115-1.1383.116-3.827
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor23.7
p_staggered_tor16.1
p_scangle_it3.745
p_mcangle_it2.847
p_planar_tor2.6
p_scbond_it2.359
p_mcbond_it1.851
p_multtor_nbd0.361
p_singtor_nbd0.181
p_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor23.7
p_staggered_tor16.1
p_scangle_it3.745
p_mcangle_it2.847
p_planar_tor2.6
p_scbond_it2.359
p_mcbond_it1.851
p_multtor_nbd0.361
p_singtor_nbd0.181
p_chiral_restr0.137
p_xyhbond_nbd0.116
p_planar_d0.041
p_angle_d0.03
p_bond_d0.013
p_plane_restr0.012
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1781
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing