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Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MP8 PDB ENTRY 1MP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M Bis-Tris, 0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.284 α = 90 b = 96.976 β = 93.3 c = 43.066 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 CCD ADSC QUANTUM 210 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.54 APS 17-ID
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 2.2 30 99.9 0.1 3.4 15582
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) 2.2 2.28 99.9 0.41 3.1 1553
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 PDB ENTRY 1MP8 2.2 30 14747 778 99.87 0.2067 0.20367 0.2017 0.26539 0.2657 RANDOM 26.211
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] -1.07 -0.06 1.09 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 22.516 r_dihedral_angle_3_deg 18.364 r_dihedral_angle_1_deg 8.203 r_scangle_it 3.409 r_scbond_it 2.198 r_mcangle_it 1.632 r_angle_refined_deg 1.572 r_mcbond_it 0.977 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 22.516 r_dihedral_angle_3_deg 18.364 r_dihedral_angle_1_deg 8.203 r_scangle_it 3.409 r_scbond_it 2.198 r_mcangle_it 1.632 r_angle_refined_deg 1.572 r_mcbond_it 0.977 r_nbtor_refined 0.301 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.195 r_symmetry_vdw_refined 0.175 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2129 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement