☰ Navigation Tabs
Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.08M sodium cacodylate, 0.16M zinc acetate, 10.4% PEG-8000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.98 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.967 α = 90 b = 34.967 β = 90 c = 64.243 γ = 120
Symmetry Space Group P 62 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 IMAGE PLATE RIGAKU RAXIS IV 2002-01-10 M SINGLE WAVELENGTH 2 1 100
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.45 30 99.3 0.034 33.5 7.1 4525 4525 -2
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 1.45 1.5 94.2 0.135 10.5
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 (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 1.45 30.29 4496 4053 443 99.38 0.18884 0.18535 0.1882 0.22388 0.2255 RANDOM 12.368
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] 0.45 0.22 0.45 -0.67
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.26 r_dihedral_angle_1_deg 3.116 r_scbond_it 2.418 r_angle_refined_deg 1.365 r_mcangle_it 1.34 r_angle_other_deg 0.733 r_mcbond_it 0.681 r_nbd_refined 0.346 r_symmetry_vdw_refined 0.341 r_xyhbond_nbd_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.26 r_dihedral_angle_1_deg 3.116 r_scbond_it 2.418 r_angle_refined_deg 1.365 r_mcangle_it 1.34 r_angle_other_deg 0.733 r_mcbond_it 0.681 r_nbd_refined 0.346 r_symmetry_vdw_refined 0.341 r_xyhbond_nbd_refined 0.293 r_symmetry_hbond_refined 0.28 r_nbd_other 0.254 r_metal_ion_refined 0.205 r_symmetry_vdw_other 0.142 r_nbtor_other 0.087 r_chiral_restr 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 157 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing