1ZUC

Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist tanaproget


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A28pdb entry 1A28

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291PEG 3350, MgSO4, PIPES pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1843.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.519α = 90
b = 64.497β = 95.76
c = 70.406γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV2002-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12301003482522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0799.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 1A2823023317833082173799.710.181220.17880.22812RANDOM22.511
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]
1.770.84-0.55-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.138
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg14.465
r_dihedral_angle_1_deg5.254
r_scangle_it4.244
r_scbond_it2.963
r_mcangle_it1.856
r_angle_refined_deg1.583
r_mcbond_it1.233
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.138
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg14.465
r_dihedral_angle_1_deg5.254
r_scangle_it4.244
r_scbond_it2.963
r_mcangle_it1.856
r_angle_refined_deg1.583
r_mcbond_it1.233
r_nbtor_refined0.305
r_symmetry_vdw_refined0.261
r_nbd_refined0.214
r_symmetry_hbond_refined0.202
r_xyhbond_nbd_refined0.134
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4070
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing