☰ Navigation Tabs
2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other ZN PEAK DATASET FROM NATIVE CRYSTAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 20% ETHANOL, 0.1M KCL, pH 7.40
Crystal Properties Matthews coefficient Solvent content 2.16 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.645 α = 90 b = 99.961 β = 90 c = 115.619 γ = 90
Symmetry Space Group C 2 2 21
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 MARRESEARCH BENT MIRRORS 2006-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 55.47 99.9 0.1 4.2 7.02 32191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.9 0.49 1.4 6.17
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 ZN PEAK DATASET FROM NATIVE CRYSTAL 2 32.03 25086 1316 99.8 0.224 0.223 0.2505 0.26 0.2763 RANDOM 23.39
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] -1.07 0.7 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.533 r_dihedral_angle_4_deg 28.852 r_dihedral_angle_3_deg 17.836 r_dihedral_angle_1_deg 5.143 r_scangle_it 4.242 r_scbond_it 2.97 r_angle_refined_deg 1.703 r_mcangle_it 1.55 r_mcbond_it 1.239 r_symmetry_hbond_refined 0.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.533 r_dihedral_angle_4_deg 28.852 r_dihedral_angle_3_deg 17.836 r_dihedral_angle_1_deg 5.143 r_scangle_it 4.242 r_scbond_it 2.97 r_angle_refined_deg 1.703 r_mcangle_it 1.55 r_mcbond_it 1.239 r_symmetry_hbond_refined 0.595 r_symmetry_vdw_refined 0.353 r_nbtor_refined 0.299 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.149 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2242 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing