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High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EE7 5EE7, 3C4M experimental model PDB 3C4M 5EE7, 3C4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 293 0.1 M sodium citrate pH 6.0, 0.3 M sodium acetate, 31% PEG400, 20 uM E-PTH(1-34)
Crystal Properties Matthews coefficient Solvent content 3.47 64.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.115 α = 80.63 b = 52.864 β = 83.76 c = 111.874 γ = 79.16
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.5 49.39 99.8 0.153 0.103 0.994 5.2 5.3 33759 50.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.3 1.662 1.214 0.501 0.9 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5EE7, 3C4M 2.5 49.386 1.97 33645 1657 99.6 0.211 0.2092 0.2123 0.2483 0.2516
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.816 f_angle_d 0.506 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4840 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 348
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing