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Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PFV PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ experimental model PDB 2LDR PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ experimental model PDB 4A49 PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ experimental model PDB 4AUQ PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BICINE, PH 9.0, 8-11% (W/V) PEG 3350 AND 0.1 M SODIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 2.63 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.97 α = 90 b = 131.8 β = 91.92 c = 122 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 6M 2012-10-15 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04 2 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 2.21 30.5 99.6 0.06 14.2 3.4 149230 2 41.76
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 2.21 2.27 99.9 0.69 2.1 3.5
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRIES 3PFV, 2LDR, 4A49 AND 4AUQ 2.21 30.54 1.34 149230 7484 99.58 0.1767 0.1748 0.1774 0.2114 0.212 48
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 13.351 f_angle_d 0.811 f_chiral_restr 0.057 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19701 Nucleic Acid Atoms Solvent Atoms 760 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PHASER phasing