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Human DYRK1A in complex with LDN-211898
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3 PDB ENTRY 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2M NA/KPO4, 20% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.955 α = 90 b = 90.891 β = 90 c = 232.468 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 PIXEL 2010-07-09 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 2.7 45.45 98.6 0.18 7.4 6.4 52473
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 2.7 2.85 95.9 0.61 2.3 5
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 2VX3 2.7 116.23 49699 2665 98.37 0.22808 0.22681 0.2298 0.25222 0.2551 RANDOM 40.729
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] 0.67 -0.66 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_1_deg 7.988 r_angle_refined_deg 1.443 r_angle_other_deg 1.227 r_mcangle_it 1.119 r_mcbond_it 0.613 r_mcbond_other 0.613 r_scbond_it 0.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_1_deg 7.988 r_angle_refined_deg 1.443 r_angle_other_deg 1.227 r_mcangle_it 1.119 r_mcbond_it 0.613 r_mcbond_other 0.613 r_scbond_it 0.561 r_chiral_restr 0.21 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.006 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_mcangle_other 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 11111 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing