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Human DDR1 in complex with a indoline inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZOS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 Protein concentration: 9.00 mg/ml
Ligand concentration: 2 mM
Complex formation: The crystals have been grown in presence of the compound
CHD-062411-2.
Drop set up: 1:1 (0.1 microL reservoir :
0.1 microL protein solution).
Crystal Properties Matthews coefficient Solvent content 2.23 44.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.89 α = 90 b = 62.44 β = 90 c = 105.05 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 100 PIXEL DECTRIS PILATUS 6M 2020-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9796 CLSI 08ID-1
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 2.588 53.67 82.4 0.282 0.282 6.9 7.9 8332
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 2.588 2.757 24.4 1.766 1.766 1.2 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.59 53.67 7902 430 82.32 0.19594 0.19235 0.1978 0.26457 0.2622 RANDOM 44.716
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] -1.65 -0.3 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.821 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 14.832 r_long_range_B_refined 7.181 r_long_range_B_other 7.172 r_dihedral_angle_1_deg 5.973 r_scangle_other 5.127 r_mcangle_other 4.943 r_mcangle_it 4.942 r_scbond_it 3.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.821 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 14.832 r_long_range_B_refined 7.181 r_long_range_B_other 7.172 r_dihedral_angle_1_deg 5.973 r_scangle_other 5.127 r_mcangle_other 4.943 r_mcangle_it 4.942 r_scbond_it 3.101 r_scbond_other 3.101 r_mcbond_it 2.989 r_mcbond_other 2.985 r_angle_refined_deg 1.212 r_angle_other_deg 0.936 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 43
Software Software Software Name Purpose XDS data reduction Aimless data scaling STARANISO data scaling REFMAC refinement PHASER phasing