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X-ray crystal structure of the K33S mutant of ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M CaCl2, 0.1 M TRIS, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.85 33.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.35 α = 69.77 b = 32.74 β = 72.55 c = 40.34 γ = 73.12
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 PSI PILATUS 6M 2013-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 23.245 98.1 0.115 0.129 8.68 4.3 19305 -3 10.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 93.7 0.09 0.108 5.88 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3H7P 1.5 23.245 2.41 19305 1931 98.4 0.1676 0.1651 0.1658 0.1901 0.1912 random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.915 f_angle_d 1.215 f_chiral_restr 0.081 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1198 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction