1W1H

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		30 % PEG 5000 MME, 0.2 M AMMONIUM SULPHATE, 0.1 M MES [PH 6.5]

Crystal Properties
Matthews coefficient	Solvent content
2	37.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.69	α = 90
b = 65.276	β = 97.49
c = 101.123	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 RAXIS4	MIRRORS	2003-06-03	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	97.5	0.05	13.2	4.5		95063		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	80.1		0.4	2.7	3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDK1PH INSP4 MODEL	1.45	30	94091	934	97.4	0.157	0.156	0.206	RANDOM	21.98

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]
0.24		0.38	-0.28		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.938
r_dihedral_angle_4_deg	15.073
r_dihedral_angle_3_deg	12.993
r_dihedral_angle_1_deg	6.697
r_scangle_it	4.983
r_scbond_it	3.817
r_mcangle_it	2.271
r_mcbond_it	1.963
r_angle_refined_deg	1.576
r_angle_other_deg	0.827
r_mcbond_other	0.724
r_symmetry_vdw_other	0.289
r_nbd_refined	0.221
r_nbd_other	0.202
r_symmetry_vdw_refined	0.192
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.108
r_nbtor_other	0.094
r_xyhbond_nbd_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	4797
Nucleic Acid Atoms
Solvent Atoms	715
Heterogen Atoms	74

Software

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