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2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SE DATASET FROM SEMET SUBSTITUTED CRYSTAL OF DIFFERENT CRYSTAL FORM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 4% PEG 400, 0.1M LITHIUM SULPHATE, 0.1M SODIUM CITRATE (PH5.6), pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.1 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.69 α = 90 b = 128.581 β = 90 c = 50.276 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 ADSC CCD TORODIAL MIRROR 2006-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 64.28 99.5 0.1 5.52 6.09 10123
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 99.5 0.41 1.81 4.6
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 SE DATASET FROM SEMET SUBSTITUTED CRYSTAL OF DIFFERENT CRYSTAL FORM 2 42.22 9619 491 99.4 0.229 0.228 0.2253 0.255 0.2481 RANDOM 29.67
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] 3.55 -2.07 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 25.916 r_dihedral_angle_3_deg 21.455 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.803 r_scbond_it 3.217 r_mcangle_it 1.796 r_angle_refined_deg 1.718 r_mcbond_it 1.487 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 25.916 r_dihedral_angle_3_deg 21.455 r_dihedral_angle_1_deg 6.087 r_scangle_it 4.803 r_scbond_it 3.217 r_mcangle_it 1.796 r_angle_refined_deg 1.718 r_mcbond_it 1.487 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.189 r_symmetry_hbond_refined 0.174 r_bond_refined_d 0.017 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 816 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing