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Crystal structure of the C-terminal domain of Vps28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1 M AS
100 mM sodium acetate
, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.84 67.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.579 α = 90 b = 117.579 β = 90 c = 294.116 γ = 120
Symmetry Space Group P 61 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 MARRESEARCH Collimating mirror+channel cut Si(111) monochromator + focussing toroidal mirror. 2004-10-10 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 diamond monochromator-germanium 220 vertically foucssing mirror - horizontally focussing multilayer mirror. 2005-01-01 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97797 ESRF BM14 2 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.05 20 99.5 24827 23615 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 3.05 3.21 99.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 3.05 19.94 23684 22301 1205 99.25 0.21599 0.21599 0.21299 0.2091 0.27269 0.2724 RANDOM 73.974
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] -0.11 -0.05 -0.11 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.328 r_dihedral_angle_3_deg 23.397 r_dihedral_angle_4_deg 19.324 r_dihedral_angle_1_deg 5.998 r_scangle_it 2.729 r_angle_refined_deg 1.749 r_scbond_it 1.674 r_mcangle_it 1.069 r_mcbond_it 0.727 r_symmetry_hbond_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.328 r_dihedral_angle_3_deg 23.397 r_dihedral_angle_4_deg 19.324 r_dihedral_angle_1_deg 5.998 r_scangle_it 2.729 r_angle_refined_deg 1.749 r_scbond_it 1.674 r_mcangle_it 1.069 r_mcbond_it 0.727 r_symmetry_hbond_refined 0.345 r_nbtor_refined 0.326 r_nbd_refined 0.258 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5390 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHELXS phasing