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Crystal structure of Cbl-b TKB domain in complex with Cblin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288 PEG 3350, BIS-TRIS, ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.144 α = 90 b = 94.091 β = 90 c = 133.949 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 100 CCD ADSC QUANTUM 210r 2010-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 2.5 50 99.9 0.143 15.3 10.7 35370 35334 -3 40.5
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 2.5 2.6 99.4 1.069 2.1 8.9
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 3OB2 2.5 47.05 32828 2448 99.88 0.20375 0.19931 0.2033 0.26397 0.2598 RANDOM 47.761
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] -0.04 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.304 r_dihedral_angle_3_deg 16.682 r_dihedral_angle_4_deg 14.987 r_long_range_B_refined 6.114 r_long_range_B_other 6.084 r_dihedral_angle_1_deg 4.383 r_scangle_other 3.545 r_mcangle_it 3.49 r_mcangle_other 3.49 r_mcbond_it 2.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.304 r_dihedral_angle_3_deg 16.682 r_dihedral_angle_4_deg 14.987 r_long_range_B_refined 6.114 r_long_range_B_other 6.084 r_dihedral_angle_1_deg 4.383 r_scangle_other 3.545 r_mcangle_it 3.49 r_mcangle_other 3.49 r_mcbond_it 2.118 r_mcbond_other 2.118 r_scbond_it 2.067 r_scbond_other 2.067 r_angle_refined_deg 0.731 r_angle_other_deg 0.509 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7493 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building