3L2J

Dimeric structure of the ligand-free extracellular domain of the human parathyroid hormone receptor (PTH1R)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C4Mpdb entry 3C4M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293ammonium sulfate, HEPES, sodium acetate, PEG400, cadaverine dihydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.702α = 90
b = 182.326β = 90
c = 97.166γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9785APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.245099.80.1112.59419648-3
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)
3.243.3698.50.4931.943.5

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 3C4M3.245019648101699.820.2270.2250.258RANDOM79.286
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]
1.1-2.070.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.37
r_dihedral_angle_4_deg22.628
r_dihedral_angle_3_deg17.635
r_dihedral_angle_1_deg5.218
r_angle_refined_deg1.078
r_scangle_it0.858
r_scbond_it0.52
r_nbtor_refined0.303
r_mcangle_it0.284
r_symmetry_hbond_refined0.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.37
r_dihedral_angle_4_deg22.628
r_dihedral_angle_3_deg17.635
r_dihedral_angle_1_deg5.218
r_angle_refined_deg1.078
r_scangle_it0.858
r_scbond_it0.52
r_nbtor_refined0.303
r_mcangle_it0.284
r_symmetry_hbond_refined0.276
r_symmetry_vdw_refined0.228
r_nbd_refined0.197
r_mcbond_it0.177
r_xyhbond_nbd_refined0.117
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7652
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing