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Integrated structural and functional model of the human ESCRT-II complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CUQ PDB ENTRY 3CUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 300 40% PEG300, 0.1M Tris-HCl, pH8.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.48 α = 90 b = 81.48 β = 90 c = 226.244 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD MARMOSAIC 300 mm CCD mirrors 2007-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 2.9 50 99.6 0.047 41.3 4.3 19966 19408 3 100.5
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 2.9 3 99.5 0.429 3.25 4.2 1915
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CUQ 2.9 40.74 19408 18368 990 99.54 0.21928 0.21423 0.2117 0.31277 0.3042 RANDOM 90.362
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.97 r_dihedral_angle_3_deg 23.497 r_dihedral_angle_4_deg 21.113 r_dihedral_angle_1_deg 7.191 r_scangle_it 2.981 r_scbond_it 1.749 r_angle_refined_deg 1.728 r_mcangle_it 1.317 r_mcbond_it 0.733 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.97 r_dihedral_angle_3_deg 23.497 r_dihedral_angle_4_deg 21.113 r_dihedral_angle_1_deg 7.191 r_scangle_it 2.981 r_scbond_it 1.749 r_angle_refined_deg 1.728 r_mcangle_it 1.317 r_mcbond_it 0.733 r_nbtor_refined 0.327 r_nbd_refined 0.271 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5055 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing