3C4M

Structure of human parathyroid hormone in complex with the extracellular domain of its G-protein-coupled receptor (PTH1R)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ANFPDB entry 1ANF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529330% PPG P400, 0.1 M NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.919α = 90
b = 116.791β = 108.8
c = 78.416γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 225 mm CCD2007-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97869APS21-ID-D

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
11.9550980.06118.133.876526-331.18
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)
11.952.0294.10.4632.15

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 1ANF1.955076488384897.920.1880.1860.227RANDOM39.311
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]
-1.56-0.341.8-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.018
r_dihedral_angle_3_deg15.481
r_dihedral_angle_4_deg14.299
r_dihedral_angle_1_deg5.368
r_scangle_it2.512
r_scbond_it1.636
r_angle_refined_deg1.187
r_mcangle_it0.943
r_mcbond_it0.609
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.018
r_dihedral_angle_3_deg15.481
r_dihedral_angle_4_deg14.299
r_dihedral_angle_1_deg5.368
r_scangle_it2.512
r_scbond_it1.636
r_angle_refined_deg1.187
r_mcangle_it0.943
r_mcbond_it0.609
r_nbtor_refined0.305
r_symmetry_vdw_refined0.239
r_nbd_refined0.194
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.142
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7723
Nucleic Acid Atoms
Solvent Atoms580
Heterogen Atoms46

Software

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