6EIP | pdb_00006eip

DYRK1A in complex with XMD8-62e


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.6152.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.95α = 90
b = 88.37β = 90
c = 229.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.984003ESRFID23-1

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
12.565098.40.1390.99610.334.957776
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)
12.562.710.8680.7451.879068

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.5648.354937279397.520.242660.241450.240.26620.26RANDOM52.174
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]
-10.5327.96-17.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.944
r_dihedral_angle_3_deg13.27
r_dihedral_angle_4_deg13.107
r_dihedral_angle_1_deg5.44
r_long_range_B_refined2.633
r_long_range_B_other2.63
r_mcangle_it1.235
r_mcangle_other1.235
r_angle_refined_deg1.145
r_angle_other_deg0.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.944
r_dihedral_angle_3_deg13.27
r_dihedral_angle_4_deg13.107
r_dihedral_angle_1_deg5.44
r_long_range_B_refined2.633
r_long_range_B_other2.63
r_mcangle_it1.235
r_mcangle_other1.235
r_angle_refined_deg1.145
r_angle_other_deg0.911
r_scangle_other0.778
r_mcbond_it0.674
r_mcbond_other0.674
r_scbond_it0.412
r_scbond_other0.412
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms10981
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing