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Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M monosaccharides, 0.1 M Buffer 1 pH 6.5, 50% Precipitant 2, Morpheus screen
Crystal Properties Matthews coefficient Solvent content 2.22 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.79 α = 90 b = 101.281 β = 90 c = 117.339 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS3 6M 2016-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97632 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.473 101.281 93.3 0.112 0.066 0.998 13.9 6.5 38315 59.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.473 2.515 99 1.155 0.667 0.796 2.1 6.9
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 4A4B 2.473 35.34 38141 1870 92.6 0.22 0.218 0.2326 0.248 0.2659 RANDOM 69.77
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] 20.8314 -16.6367 -4.1947
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.01 t_omega_torsion 2.1 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.01 t_omega_torsion 2.1 t_angle_deg 0.95 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 7384 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 70
Software Software Software Name Purpose BUSTER refinement xia2 data reduction Aimless data scaling PHASER phasing