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Structure of human parathyroid hormone in complex with the extracellular domain of its G-protein-coupled receptor (PTH1R)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANF PDB entry 1ANF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% PPG P400, 0.1 M NaCacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.919 α = 90 b = 116.791 β = 108.8 c = 78.416 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2007-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97869 APS 21-ID-D
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 1.95 50 98 0.061 18.13 3.8 76526 -3 31.18
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 1.95 2.02 94.1 0.463 2.15
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 1ANF 1.95 50 76488 3848 97.92 0.188 0.186 0.1867 0.227 0.2266 RANDOM 39.311
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 -0.34 1.8 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_3_deg 15.481 r_dihedral_angle_4_deg 14.299 r_dihedral_angle_1_deg 5.368 r_scangle_it 2.512 r_scbond_it 1.636 r_angle_refined_deg 1.187 r_mcangle_it 0.943 r_mcbond_it 0.609 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.018 r_dihedral_angle_3_deg 15.481 r_dihedral_angle_4_deg 14.299 r_dihedral_angle_1_deg 5.368 r_scangle_it 2.512 r_scbond_it 1.636 r_angle_refined_deg 1.187 r_mcangle_it 0.943 r_mcbond_it 0.609 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7723 Nucleic Acid Atoms Solvent Atoms 580 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