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Human DDR1 in complex with a pyrrolidine 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 277 Protein concentration: 10 mg/ml
Ligand concentration: 10 mM
Complex formation: The crystals have been grown in presence of the
compound CHD-070065.
Drop set up: 1:1 (0.1 microL reservoir : 0.1 microL protein solution).
Crystal Properties Matthews coefficient Solvent content 2.13 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.517 α = 90 b = 68.725 β = 90 c = 70.429 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 EIGER X 16M 2021-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
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 2.117 49.19 100 0.268 0.268 6.9 6.8 17583
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 2.117 2.153 100 1.736 1.736 1.3 7
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 2.12 49.19 16701 871 99.89 0.21524 0.21301 0.2161 0.2573 0.2576 RANDOM 32.982
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] -2.77 -0.02 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.492 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 7.1 r_long_range_B_refined 3.526 r_long_range_B_other 3.522 r_angle_refined_deg 1.473 r_angle_other_deg 1.183 r_mcangle_it 0.962 r_mcangle_other 0.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.492 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 7.1 r_long_range_B_refined 3.526 r_long_range_B_other 3.522 r_angle_refined_deg 1.473 r_angle_other_deg 1.183 r_mcangle_it 0.962 r_mcangle_other 0.962 r_scangle_other 0.782 r_mcbond_it 0.527 r_mcbond_other 0.527 r_scbond_it 0.446 r_scbond_other 0.446 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 2336 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 55
Software Software Software Name Purpose XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing Coot model building