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Crystal structure of GDNF-GFRalpha1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V5E PDB entry 2V5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 15% PEG4000, 0.15 M (NH4)2SO4, 0.1 M MES buffer pH 6, Vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.2 α = 90 b = 84.1 β = 96.1 c = 179.2 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 210 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.35 42 97 0.09 3.8 31756 30497 1 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.45 91.3 0.43 2.95 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2V5E 2.35 20 31756 25681 1358 97.05 0.22834 0.22554 0.28021 0.2202 RANDOM 24.308
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] -0.04 0.19 -1.31 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_4_deg 14.737 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.655 r_scbond_it 2.301 r_mcangle_it 1.561 r_angle_refined_deg 1.091 r_mcbond_it 0.839 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_3_deg 16.918 r_dihedral_angle_4_deg 14.737 r_dihedral_angle_1_deg 5.493 r_scangle_it 3.655 r_scbond_it 2.301 r_mcangle_it 1.561 r_angle_refined_deg 1.091 r_mcbond_it 0.839 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4561 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 59
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction