6EJ4 | pdb_00006ej4

DYRK1A in complex with XMD7-112


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NCT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M KSCN; 0.05M NaCl; 16% PEG 3350, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.6152.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.15α = 90
b = 88.19β = 90
c = 229.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976251ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.885098.80.1660.9939.85540869
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.883.0595.30.6910.7931.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4nct2.8848.338847202098.760.222460.219990.220.270190.27RANDOM57.455
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]
7.1449.13-56.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.461
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg16.549
r_dihedral_angle_1_deg6.571
r_long_range_B_refined2.621
r_long_range_B_other2.621
r_angle_refined_deg1.27
r_mcangle_it1.217
r_mcangle_other1.217
r_angle_other_deg0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.461
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg16.549
r_dihedral_angle_1_deg6.571
r_long_range_B_refined2.621
r_long_range_B_other2.621
r_angle_refined_deg1.27
r_mcangle_it1.217
r_mcangle_other1.217
r_angle_other_deg0.939
r_scangle_other0.729
r_mcbond_it0.671
r_mcbond_other0.671
r_scbond_it0.383
r_scbond_other0.383
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms10878
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing