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The X-ray crystal structure of human endothelin-1, a polypeptide hormone regulator of blood pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GLH PDB entry 5GLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 310 4 uL 15 mg/mL aqueous endothelin + 6 uL reservoir solution (20-25% MPD, 0.2 M MES, pH 6.5) + 2 uL 0.2 M MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.71 29.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.328 α = 90 b = 27.328 β = 90 c = 79.538 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 AREA DETECTOR SDMS 1997-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.85 80 99.6 0.257 0.257 0.283 0.086 0.947 4.6 7.7 2534
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 5GLH 1.85 23.67 2534 143 92.92 0.2079 0.20387 0.2165 0.28373 0.2911 RANDOM 32.583
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] 0.01 0.01 0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.176 r_dihedral_angle_3_deg 20.16 r_dihedral_angle_1_deg 8.03 r_long_range_B_refined 7.759 r_long_range_B_other 7.752 r_mcangle_it 4.635 r_mcangle_other 4.629 r_scangle_other 3.994 r_mcbond_it 3.171 r_mcbond_other 3.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.176 r_dihedral_angle_3_deg 20.16 r_dihedral_angle_1_deg 8.03 r_long_range_B_refined 7.759 r_long_range_B_other 7.752 r_mcangle_it 4.635 r_mcangle_other 4.629 r_scangle_other 3.994 r_mcbond_it 3.171 r_mcbond_other 3.144 r_scbond_it 2.696 r_scbond_other 2.69 r_angle_refined_deg 1.632 r_angle_other_deg 0.883 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 334 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SDMS data reduction Aimless data scaling PHASER phasing