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Crystal structure of EDA-A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D0G truncated model of Apo2L/TRAIL from 1d0g
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 20% PEG 3350, 0.2M di-sodium hydrogen phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.657 α = 90 b = 279.687 β = 91.36 c = 54.175 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 100 IMAGE PLATE MARRESEARCH 2002-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 30 94.5 0.081 0.081 8.6 3.2 70270 66402 -3 31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 94.5 0.24 0.24 3 3.1 6606
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 (All) 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 truncated model of Apo2L/TRAIL from 1d0g 2.3 20 59179 59179 7099 94.27 0.2012 0.20127 0.19424 0.1974 0.26029 0.2592 THIN SHELLS 6.026
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] -0.93 0.1 -0.24 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.998 r_scangle_it 3.523 r_scbond_it 2.521 r_mcangle_it 2.4 r_mcbond_it 1.672 r_angle_refined_deg 1.304 r_angle_other_deg 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.998 r_scangle_it 3.523 r_scbond_it 2.521 r_mcangle_it 2.4 r_mcbond_it 1.672 r_angle_refined_deg 1.304 r_angle_other_deg 0.794 r_symmetry_vdw_other 0.289 r_nbd_other 0.255 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.165 r_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13548 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing