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Structure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293
Crystal Properties Matthews coefficient Solvent content 1.84 33.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.222 α = 90 b = 29.479 β = 94.31 c = 45.756 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 113 IMAGE PLATE RIGAKU RAXIS IV++ 2014-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5
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 1.8 50 99.1 0.144 38.055 3.5 11478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83
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 1cka 1.8 45.63 10714 612 98.81 0.17323 0.16964 0.1859 0.24252 0.2489 RANDOM 20.533
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] -0.52 0.1 -0.03 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.848 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 12.171 r_long_range_B_refined 6.45 r_dihedral_angle_1_deg 6.132 r_long_range_B_other 5.884 r_scangle_other 4.236 r_angle_other_deg 3.453 r_scbond_other 2.927 r_scbond_it 2.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.848 r_dihedral_angle_4_deg 17.973 r_dihedral_angle_3_deg 12.171 r_long_range_B_refined 6.45 r_dihedral_angle_1_deg 6.132 r_long_range_B_other 5.884 r_scangle_other 4.236 r_angle_other_deg 3.453 r_scbond_other 2.927 r_scbond_it 2.792 r_mcangle_it 2.096 r_mcangle_other 2.096 r_angle_refined_deg 2.039 r_mcbond_it 1.538 r_mcbond_other 1.536 r_chiral_restr 0.113 r_gen_planes_other 0.024 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 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 1146 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing