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Crystal structure of the tyrosine kinase binding domain of Cbl-c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 16% PEG3350, 0.1M ammonium formate, 0.2M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.223 α = 90 b = 107.617 β = 90 c = 54.773 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD Bruker DIP-6040 2007-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.64 50 100 0.054 0.054 27.992 4.3 34203 -3 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 100 0.446 0.446 3.452 4.3 1688
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 2CBL 1.64 43.24 34184 1728 99.81 0.1834 0.1816 0.181 0.2177 0.218 RANDOM 20.2597
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 r_dihedral_angle_2_deg 34.362 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 13.063 r_scangle_it 5.727 r_dihedral_angle_1_deg 5.316 r_scbond_it 3.727 r_mcangle_it 2.404 r_angle_refined_deg 1.849 r_mcbond_it 1.358 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.362 r_dihedral_angle_3_deg 13.697 r_dihedral_angle_4_deg 13.063 r_scangle_it 5.727 r_dihedral_angle_1_deg 5.316 r_scbond_it 3.727 r_mcangle_it 2.404 r_angle_refined_deg 1.849 r_mcbond_it 1.358 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 1
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction