☰ Navigation Tabs
Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 50 mM sodium cacodylate, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.699 α = 90 b = 41.699 β = 90 c = 69.831 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9797 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.538 36.113 99.7 0.067 0.08 0.044 10.2 3.1 20124 20124
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.538 1.62 98.8 0.333 0.333 0.235 2.1 2.8 2910
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UBQ 1.54 25.1 19062 1035 99.66 0.1403 0.1386 0.1727 0.2251 RANDOM 16.231
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] 3.12 3.12 -6.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.303 r_dihedral_angle_4_deg 13.52 r_dihedral_angle_3_deg 11.631 r_dihedral_angle_1_deg 6.234 r_mcangle_it 2.943 r_mcbond_it 2.542 r_mcbond_other 2.504 r_angle_refined_deg 1.825 r_angle_other_deg 1.247 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.303 r_dihedral_angle_4_deg 13.52 r_dihedral_angle_3_deg 11.631 r_dihedral_angle_1_deg 6.234 r_mcangle_it 2.943 r_mcbond_it 2.542 r_mcbond_other 2.504 r_angle_refined_deg 1.825 r_angle_other_deg 1.247 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1166 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction