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Structure of the DDR1 kinase domain in complex with ponatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AT5 PDB ENTRY 4AT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M BIS-TRIS PH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.951 α = 90 b = 61.733 β = 104.4 c = 80.193 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 100 PIXEL DECTRIS PILATUS 2M 2013-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.92 45.37 99 0.14 9.1 6.1 49502 2
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 1.92 1.97 98.7 0.78 2.7 6.1
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 4AT5 1.92 45.41 46866 2507 98.64 0.20757 0.20613 0.2129 0.23416 0.2421 RANDOM 22.707
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] 1.91 0.57 -0.87 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.488 r_angle_other_deg 1.033 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.473 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.488 r_angle_other_deg 1.033 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4730 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing