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Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EXE PDB ENTRY 1EXE AND 1Z57 experimental model PDB 1Z57 PDB ENTRY 1EXE AND 1Z57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 34% PEG 300, 0.1 M LISO4, TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 3.02 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 264.203 α = 90 b = 65.105 β = 115.44 c = 140.282 γ = 90
Symmetry Space Group C 1 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 MARRESEARCH 2008-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.4 26.35 99.9 0.08 10.2 3.5 92815 2 55.7
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) 1 2.4 2.53 99.9 0.68 2 3.5
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 1EXE AND 1Z57 2.4 26 82846 1799 99.9 0.186 0.185 0.1875 0.23 0.2309 RANDOM 27
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] 0.39 -1.13 0.4 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.901 r_dihedral_angle_4_deg 20.285 r_dihedral_angle_3_deg 14.738 r_scangle_it 7.017 r_dihedral_angle_1_deg 5.867 r_scbond_it 5.643 r_mcangle_it 2.988 r_mcbond_it 1.781 r_angle_refined_deg 1.518 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.901 r_dihedral_angle_4_deg 20.285 r_dihedral_angle_3_deg 14.738 r_scangle_it 7.017 r_dihedral_angle_1_deg 5.867 r_scbond_it 5.643 r_mcangle_it 2.988 r_mcbond_it 1.781 r_angle_refined_deg 1.518 r_angle_other_deg 0.919 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11050 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing