3D48

Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BP3FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental modelPDB 1F6FFOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental modelPDB 1RW5FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.
experimental modelPDB 1N9DFOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52973.5M Sodium Chloride, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
3.4163.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.35α = 90
b = 125.35β = 90
c = 69.82γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0000MAX III911-3

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
12.52099.80.08322.4611.22176321797-3-346.4
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)
2.52.561000.5015.511.221797

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.2.5202171720629108899.870.2210.2210.2180.295RANDOM46.307
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]
-2.48-1.24-2.483.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_3_deg22.244
r_dihedral_angle_4_deg20.394
r_dihedral_angle_1_deg8.69
r_scangle_it4.035
r_scbond_it2.465
r_angle_refined_deg2.013
r_mcangle_it1.782
r_mcbond_it0.964
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.912
r_dihedral_angle_3_deg22.244
r_dihedral_angle_4_deg20.394
r_dihedral_angle_1_deg8.69
r_scangle_it4.035
r_scbond_it2.465
r_angle_refined_deg2.013
r_mcangle_it1.782
r_mcbond_it0.964
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2945
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing