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Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand
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 286 Lithium sulfate monohydrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.86 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.6 α = 90 b = 41.34 β = 90 c = 56.82 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 113 IMAGE PLATE RIGAKU 2015-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 33.43 100 0.16 0.977 11.7 7.4 6759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.87 99.9 0.2 0.96 8.4 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1cka 1.77 33.43 6462 264 99.96 0.17587 0.17439 0.21037 0.2739 RANDOM 13.616
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] 0.11 0.07 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.067 r_dihedral_angle_3_deg 14.641 r_dihedral_angle_4_deg 11.588 r_long_range_B_other 6.781 r_long_range_B_refined 6.769 r_dihedral_angle_1_deg 5.509 r_scangle_other 4.204 r_angle_other_deg 3.556 r_scbond_it 2.708 r_scbond_other 2.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.067 r_dihedral_angle_3_deg 14.641 r_dihedral_angle_4_deg 11.588 r_long_range_B_other 6.781 r_long_range_B_refined 6.769 r_dihedral_angle_1_deg 5.509 r_scangle_other 4.204 r_angle_other_deg 3.556 r_scbond_it 2.708 r_scbond_other 2.708 r_angle_refined_deg 2.611 r_mcangle_other 2.564 r_mcangle_it 2.56 r_mcbond_it 1.66 r_mcbond_other 1.544 r_chiral_restr 0.138 r_bond_refined_d 0.029 r_gen_planes_other 0.028 r_gen_planes_refined 0.012 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 616 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing