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DYRK1A in complex with XMD7-117
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; 0.1M NaCl; 14% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.44 α = 90 b = 88.536 β = 90 c = 231.142 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) 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 2.22 50 99.1 0.149 8.6 4.9 89260
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 1.93 2.22 96.2 0.775 0.743 1.93 13806
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 2.22 48.57 84728 4529 99.12 0.21998 0.21836 0.2102 0.25049 0.2084 RANDOM 46.94
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] -14.63 5.37 9.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.773 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 12.647 r_dihedral_angle_1_deg 5.029 r_long_range_B_refined 2.869 r_long_range_B_other 2.832 r_angle_refined_deg 1.076 r_mcangle_it 1.013 r_mcangle_other 1.013 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.773 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 12.647 r_dihedral_angle_1_deg 5.029 r_long_range_B_refined 2.869 r_long_range_B_other 2.832 r_angle_refined_deg 1.076 r_mcangle_it 1.013 r_mcangle_other 1.013 r_angle_other_deg 0.86 r_scangle_other 0.632 r_mcbond_it 0.557 r_mcbond_other 0.557 r_scbond_it 0.346 r_scbond_other 0.346 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 10771 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing