3PWY | pdb_00003pwy

Crystal structure of an extender (SPD28345)-modified human PDK1 complex 2

X-RAY DIFFRACTION

---

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	VAPOR DIFFUSION, HANGING DROP	7.4	293	0.1 M Tris pH 7.4, 2.1 M ammonium sulfate; 16 mg/ml protein in 50 mM Tris pH 8, 400 mM KCl, 3 mM DTT; supplemented with 20 mM DTT prior to addition of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.376	α = 90
b = 122.376	β = 90
c = 47.632	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	200	CCD	ADSC QUANTUM 315	1-m-long Rh-coated bent cylindrical mirror for horizontal and vertical focusing	2006-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5		SSRL	BL1-5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.5	100	93.7	0.135	5.2	2.9	14428	5005	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3.5	20	5005	4491	476	93.38	0.22572	0.22014	0.21	0.27649	0.27	RANDOM	32.27

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]
2.18	1.09		2.18		-3.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.295
r_dihedral_angle_3_deg	13.675
r_dihedral_angle_4_deg	11.868
r_dihedral_angle_1_deg	4.598
r_angle_refined_deg	0.868
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.216
r_nbd_refined	0.171
r_xyhbond_nbd_refined	0.138
r_symmetry_vdw_refined	0.127
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2265
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	18

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling