1W1G | pdb_00001w1g

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.2		25 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.1	0.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.264	α = 90
b = 58.943	β = 102.33
c = 36.44	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS 4	MIRRORS	2003-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.45	30	99.7	0.05	8.8	2.9		25810		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.5	100		0.37	2.5	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDK1PH INSP4 MODEL	1.45	25	25241	545	99.7	0.183	0.182	0.2	0.236	0.25	RANDOM	26.94

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]
1.58		0.06	-0.83		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.693
r_dihedral_angle_4_deg	17.708
r_dihedral_angle_3_deg	13.71
r_dihedral_angle_1_deg	6.622
r_scangle_it	4.923
r_scbond_it	3.614
r_mcangle_it	2.305
r_mcbond_it	1.727
r_angle_refined_deg	1.703
r_angle_other_deg	0.86
r_mcbond_other	0.745
r_symmetry_hbond_refined	0.274
r_symmetry_vdw_other	0.24
r_nbd_refined	0.221
r_nbd_other	0.2
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.109
r_nbtor_other	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_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 Atoms	Number
Protein Atoms	1194
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing