1UU3 | pdb_00001uu3

Structure of human PDK1 kinase domain in complex with LY333531

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		2.1 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 7.2

Crystal Properties
Matthews coefficient	Solvent content
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.623	α = 90
b = 121.623	β = 90
c = 47.875	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	1.7	25	99.9	0.044	22.1	4.9		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	1.7	1.76	98.6		0.278	4.7	3.7

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	PDB ENTRY 1H1W	1.7	25	42657	661	96.9	0.174	0.173	0.18	0.202	0.22	RANDOM	17.71

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]
0.57	0.28		0.57		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.943
r_scangle_it	4.225
r_scbond_it	2.653
r_mcangle_it	1.826
r_angle_refined_deg	1.65
r_mcbond_it	1.035
r_angle_other_deg	0.877
r_symmetry_vdw_other	0.257
r_nbd_other	0.244
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.116
r_nbtor_other	0.081
r_bond_refined_d	0.015
r_gen_planes_other	0.015
r_gen_planes_refined	0.012
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	2249
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	118

Software

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