1W1H

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.530 % PEG 5000 MME, 0.2 M AMMONIUM SULPHATE, 0.1 M MES [PH 6.5]
Crystal Properties
Matthews coefficientSolvent content
237.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.69α = 90
b = 65.276β = 97.49
c = 101.123γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS4MIRRORS2003-06-03MSINGLE 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
11.453097.50.0513.24.5950632
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)
11.451.580.10.42.73

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 REPLACEMENTTHROUGHOUTPDK1PH INSP4 MODEL1.45309409193497.40.1570.1560.206RANDOM21.98
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]
0.240.38-0.280.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.938
r_dihedral_angle_4_deg15.073
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg6.697
r_scangle_it4.983
r_scbond_it3.817
r_mcangle_it2.271
r_mcbond_it1.963
r_angle_refined_deg1.576
r_angle_other_deg0.827
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.938
r_dihedral_angle_4_deg15.073
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg6.697
r_scangle_it4.983
r_scbond_it3.817
r_mcangle_it2.271
r_mcbond_it1.963
r_angle_refined_deg1.576
r_angle_other_deg0.827
r_mcbond_other0.724
r_symmetry_vdw_other0.289
r_nbd_refined0.221
r_nbd_other0.202
r_symmetry_vdw_refined0.192
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.162
r_chiral_restr0.108
r_nbtor_other0.094
r_xyhbond_nbd_other0.084
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms4797
Nucleic Acid Atoms
Solvent Atoms715
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing