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DYRK1A in complex with XMD7-112
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M KSCN; 0.05M NaCl; 16% PEG 3350, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.15 α = 90 b = 88.19 β = 90 c = 229.2 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 PILATUS3 6M 2016-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976251 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.88 50 98.8 0.166 0.993 9.85 5 40869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.88 3.05 95.3 0.691 0.793 1.96
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 4nct 2.88 48.3 38847 2020 98.76 0.22246 0.21999 0.2193 0.27019 0.2654 RANDOM 57.455
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] 7.14 49.13 -56.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 16.549 r_dihedral_angle_1_deg 6.571 r_long_range_B_refined 2.621 r_long_range_B_other 2.621 r_angle_refined_deg 1.27 r_mcangle_it 1.217 r_mcangle_other 1.217 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 16.549 r_dihedral_angle_1_deg 6.571 r_long_range_B_refined 2.621 r_long_range_B_other 2.621 r_angle_refined_deg 1.27 r_mcangle_it 1.217 r_mcangle_other 1.217 r_angle_other_deg 0.939 r_scangle_other 0.729 r_mcbond_it 0.671 r_mcbond_other 0.671 r_scbond_it 0.383 r_scbond_other 0.383 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10878 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing