3ION | pdb_00003ion

PDK1 in complex with Compound 8h

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	293	VAPOR DIFFUSION, HANGING DROP, pH 8.6, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.368	α = 90
b = 123.368	β = 90
c = 47.265	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	93	CCD	RIGAKU SATURN 92		2005-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	100					15542

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.4	26.71	15542	827	99.71	0.2464	0.24454	0.2424	0.28179	0.2771	RANDOM	33.831

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]
0.87	0.44		0.87		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.496
r_dihedral_angle_4_deg	21.37
r_dihedral_angle_3_deg	15.083
r_dihedral_angle_1_deg	5.286
r_scangle_it	1.325
r_angle_refined_deg	1.026
r_scbond_it	0.776
r_mcangle_it	0.769
r_mcbond_it	0.429
r_nbtor_refined	0.303
r_nbd_refined	0.17
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.106
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2239
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling