2VKI

Structure of the PDK1 PH domain K465E mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2 M LITHIUM SULPHATE, 0.1 M TRIS HYDROCHLORIDE [PH 8.5] 30 % (W/V) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.009α = 90
b = 67.057β = 90
c = 67.802γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE2004-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.8251000.06104.5149502
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)
11.81.861000.552.34.3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1W1D1.8251430960999.50.1750.1730.215RANDOM21.05
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]
0.12-0.640.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.298
r_scangle_it4.059
r_scbond_it2.542
r_mcangle_it1.78
r_angle_refined_deg1.681
r_mcbond_it0.983
r_angle_other_deg0.904
r_symmetry_vdw_other0.312
r_nbd_other0.253
r_nbd_refined0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.298
r_scangle_it4.059
r_scbond_it2.542
r_mcangle_it1.78
r_angle_refined_deg1.681
r_mcbond_it0.983
r_angle_other_deg0.904
r_symmetry_vdw_other0.312
r_nbd_other0.253
r_nbd_refined0.216
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.117
r_chiral_restr0.106
r_nbtor_other0.086
r_bond_refined_d0.016
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
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 Atoms1172
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing