1UU7

Structure of human PDK1 kinase domain in complex with BIM-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H1W	PDB ENTRY 1H1W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		2.3 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 8.25

Crystal Properties
Matthews coefficient	Solvent content
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.947	α = 90
b = 121.947	β = 90
c = 48.071	γ = 120

Symmetry
Space Group	P 32 2 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	CCD	ADSC CCD		2003-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.9	30	99.9	0.076	10	3.7		44644

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	1.9	1.97	99.8		0.592	2.7	3.5

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	PDB ENTRY 1H1W	1.9	30	31794	669	99.8	0.235	0.234	0.279	RANDOM	18.42

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]
0.46	0.23		0.46		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.434
r_scangle_it	3.539
r_scbond_it	2.268
r_angle_refined_deg	1.602
r_mcangle_it	1.473
r_angle_other_deg	0.871
r_mcbond_it	0.826
r_symmetry_hbond_refined	0.263
r_nbd_other	0.243
r_symmetry_vdw_refined	0.221
r_symmetry_vdw_other	0.217
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.094
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.002
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 Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing