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Dimeric structure of the ligand-free extracellular domain of the human parathyroid hormone receptor (PTH1R)
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, HANGING DROP 7.5 293 ammonium sulfate, HEPES, sodium acetate, PEG400, cadaverine dihydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.702 α = 90 b = 182.326 β = 90 c = 97.166 γ = 90
Symmetry Space Group C 2 2 21
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 3.24 50 99.8 0.11 12.59 4 19648 -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) 3.24 3.36 98.5 0.493 1.94 3.5
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 3.24 50 19648 1016 99.82 0.227 0.225 0.2232 0.258 0.253 RANDOM 79.286
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 -2.07 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_4_deg 22.628 r_dihedral_angle_3_deg 17.635 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.078 r_scangle_it 0.858 r_scbond_it 0.52 r_nbtor_refined 0.303 r_mcangle_it 0.284 r_symmetry_hbond_refined 0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_4_deg 22.628 r_dihedral_angle_3_deg 17.635 r_dihedral_angle_1_deg 5.218 r_angle_refined_deg 1.078 r_scangle_it 0.858 r_scbond_it 0.52 r_nbtor_refined 0.303 r_mcangle_it 0.284 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.197 r_mcbond_it 0.177 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7652 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing