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Crystal structure of the extracellular domain of the human parathyroid hormone receptor (PTH1R) in complex with parathyroid hormone-related protein (PTHrP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C4M pdb entry 3C4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 7.5% PEG 2000, 13% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.041 α = 90 b = 84.041 β = 90 c = 164.455 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9785 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.94 50 91.2 0.091 29.66 17 40884 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.01 55 0.443 2.25 8.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3C4M 1.94 50 40693 2065 91.58 0.195 0.193 0.1921 0.233 0.2348 RANDOM 44.976
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] 1.48 1.48 -2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.87 r_dihedral_angle_4_deg 18.828 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_1_deg 5.664 r_scangle_it 2.858 r_scbond_it 1.855 r_angle_refined_deg 1.264 r_mcangle_it 1.097 r_mcbond_it 0.713 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.87 r_dihedral_angle_4_deg 18.828 r_dihedral_angle_3_deg 16.06 r_dihedral_angle_1_deg 5.664 r_scangle_it 2.858 r_scbond_it 1.855 r_angle_refined_deg 1.264 r_mcangle_it 1.097 r_mcbond_it 0.713 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3889 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling