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Human Ubc9 with covalent isopeptide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293.15 0.1 M trisodium citrate pH 5.0, 30% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.7 α = 90 b = 38.7 β = 118.9 c = 97.8 γ = 90
Symmetry Space Group P 1 21 1
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 2M-F 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.9 47 99.1 0.062 0.074 0.999 13.2 3.307 49319 23.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99 0.394 0.473 0.846 3.49 3.242
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 5f6e 1.9 47 49318 2466 99.3 0.2153 0.2129 0.1913 0.263 0.2148 RANDOM 30.76
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] 1.7882 -1.7025 4.4199 -6.2081
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.62 t_omega_torsion 3 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.62 t_omega_torsion 3 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5280 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction