1UNG | pdb_00001ung

Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H4LPDB ENTRY 1H4L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1713% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT
Crystal Properties
Matthews coefficientSolvent content
2.856.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.724α = 90
b = 117.724β = 90
c = 156.794γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC CCD2002-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.32595.40.1049.16.2537312.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.497.50.372.62.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1H4L2.319.7650923271395.50.2160.2160.210.2250.22RANDOM22.42
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]
-0.08-0.04-0.080.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it3.902
r_angle_other_deg3.697
r_scbond_it2.625
r_angle_refined_deg1.871
r_mcangle_it1.477
r_mcbond_it0.812
r_symmetry_vdw_other0.353
r_nbd_other0.304
r_symmetry_hbond_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.22
r_scangle_it3.902
r_angle_other_deg3.697
r_scbond_it2.625
r_angle_refined_deg1.871
r_mcangle_it1.477
r_mcbond_it0.812
r_symmetry_vdw_other0.353
r_nbd_other0.304
r_symmetry_hbond_refined0.248
r_nbd_refined0.236
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_refined0.18
r_chiral_restr0.121
r_nbtor_other0.111
r_bond_refined_d0.02
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 AtomsNumber
Protein Atoms6870
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing