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Structural basis for angiopoietin-1 mediated signaling initiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z3S PDB ENTRY 1Z3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.0 M Na/K-tartate, 0.1 M Tris, 0.2 M LiSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.968 α = 90 b = 80.968 β = 90 c = 187.216 γ = 120
Symmetry Space Group P 64 2 2
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 315 2009-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.5 70.12 98.9 0.079 24.1 4 13340 13192
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 2.5 2.59 99.3 0.42 3 4 1279
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 1Z3S 2.5 30 12559 649 99.26 0.18894 0.18637 0.1912 0.24231 0.2284 RANDOM 48.277
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] 2.02 1.01 2.02 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.773 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 8.321 r_scangle_it 5.233 r_scbond_it 3.397 r_mcangle_it 2.188 r_angle_refined_deg 2.057 r_mcbond_it 1.18 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.773 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 8.321 r_scangle_it 5.233 r_scbond_it 3.397 r_mcangle_it 2.188 r_angle_refined_deg 2.057 r_mcbond_it 1.18 r_chiral_restr 0.139 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 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 1754 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling