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Crystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AL6 PDB ENTRY 2AL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 1 M AMMONIUM CITRATE TRIBASIC, pH 7.0, 0.1 M BIS-TRIS PROPANE pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.19 70.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.971 α = 90 b = 112.971 β = 90 c = 103.335 γ = 120
Symmetry Space Group P 32 2 1
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 MARMOSAIC 300 mm CCD ROSENBAUM-ROCH DOUBLE XTAL 2009-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 3.25 49.564 99.94 0.113 0.113 22.8 11 12393 12393 -3 85.6
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 3.25 3.37 100 0.774 0.744 3 8.7 715
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2AL6 3.25 49.564 12393 12393 546 99.98 0.1872 0.1872 0.1861 0.1792 0.2121 0.1988 RANDOM 90.463
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] -0.53 -0.27 -0.53 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.58 r_dihedral_angle_3_deg 24.733 r_dihedral_angle_4_deg 22.12 r_dihedral_angle_1_deg 8.337 r_scangle_it 4.128 r_scbond_it 2.33 r_angle_refined_deg 2.215 r_mcangle_it 1.801 r_mcbond_it 0.934 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.58 r_dihedral_angle_3_deg 24.733 r_dihedral_angle_4_deg 22.12 r_dihedral_angle_1_deg 8.337 r_scangle_it 4.128 r_scbond_it 2.33 r_angle_refined_deg 2.215 r_mcangle_it 1.801 r_mcbond_it 0.934 r_chiral_restr 0.144 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2813 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling