3DND | pdb_00003dnd

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	277	75mM LiCl, 30mM MesBisTris, 1mM DTT, 0.2mM EDTA, pH 6.5, 15% Methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.045	α = 90
b = 77.649	β = 90
c = 80.088	γ = 90

Symmetry
Space Group	P 21 21 21

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 QUANTUM 4		2008-03-06	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)	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	2.26	77.6	99.9			21932	21900	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.33	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	2.26	34.94	21932	20377	1521	99.87	0.19	0.19348	0.18901	0.1881	0.25324	0.2525	RANDOM	31.004

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]
0.05			-0.11		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.395
r_dihedral_angle_4_deg	25.953
r_dihedral_angle_3_deg	18.856
r_dihedral_angle_1_deg	6.457
r_scangle_it	4.342
r_scbond_it	2.808
r_mcangle_it	1.886
r_angle_refined_deg	1.849
r_mcbond_it	1.136
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2937
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing