6EIQ | pdb_00006eiq

DYRK1A in complex with XMD14-124


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; 0.1M NaCl; 12% PEG 3350, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.56α = 90
b = 87.6β = 90
c = 229.04γ = 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)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
12.35097.19.453.877090
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)
12.32.4497.51.2060.4190.9912348

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 REPLACEMENTTHROUGHOUT4nct2.348.173223384696.980.219860.218120.220.252450.25RANDOM55.491
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]
11.3325.45-36.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.521
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg14.988
r_dihedral_angle_1_deg6.109
r_long_range_B_refined2.985
r_long_range_B_other2.963
r_mcangle_it1.558
r_mcangle_other1.558
r_angle_refined_deg1.297
r_scangle_other1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.521
r_dihedral_angle_4_deg17.433
r_dihedral_angle_3_deg14.988
r_dihedral_angle_1_deg6.109
r_long_range_B_refined2.985
r_long_range_B_other2.963
r_mcangle_it1.558
r_mcangle_other1.558
r_angle_refined_deg1.297
r_scangle_other1.164
r_angle_other_deg0.981
r_mcbond_it0.896
r_mcbond_other0.896
r_scbond_it0.68
r_scbond_other0.68
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
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 Atoms10948
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing