4NCT | pdb_00004nct

Human DYRK1A in complex with PKC412


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82930.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.764α = 90
b = 87.895β = 90
c = 229.921γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
12.59748.2599.75579755625-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5972.7598.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUT2.59748.255297952841278299.740.21010.208050.1950.249460.2258RANDOM49.922
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]
-3.8617.24-13.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg16.449
r_dihedral_angle_3_deg13.694
r_dihedral_angle_1_deg5.352
r_long_range_B_refined3.994
r_long_range_B_other3.977
r_mcangle_it2.145
r_mcangle_other2.141
r_scangle_other2.031
r_mcbond_it1.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.729
r_dihedral_angle_4_deg16.449
r_dihedral_angle_3_deg13.694
r_dihedral_angle_1_deg5.352
r_long_range_B_refined3.994
r_long_range_B_other3.977
r_mcangle_it2.145
r_mcangle_other2.141
r_scangle_other2.031
r_mcbond_it1.222
r_mcbond_other1.222
r_scbond_other1.138
r_scbond_it1.124
r_angle_refined_deg1.11
r_angle_other_deg0.708
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 Atoms11042
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms172

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling