3E8C | pdb_00003e8c

Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		273	13-17% PEG 3K-20K, 100 mM MES pH 6.5 or acetate 4.6, 1-15% methanol. Seeded, pH 4.5 - 6.5, vapor diffusion, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.46	α = 90
b = 96.392	β = 102.66
c = 180.036	γ = 90

Symmetry
Space Group	P 1 21 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 QUANTUM 210	un-focused beam	2005-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	2.2	50	98.2	0.079		4.3		137412		2

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	2.2	2.28	97.3		0.6		4.2

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		THROUGHOUT	2.2	46.93	127573	6773	95.82	0.26499	0.26365	0.2625	0.28988	0.2856	RANDOM	14.349

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]
-1.65		-1.98	-0.35		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.604
r_dihedral_angle_4_deg	18.049
r_dihedral_angle_3_deg	15.535
r_dihedral_angle_1_deg	5.044
r_angle_refined_deg	1.195
r_angle_other_deg	0.928
r_scangle_it	0.788
r_scbond_it	0.519
r_mcangle_it	0.405
r_mcbond_it	0.253
r_symmetry_vdw_other	0.238
r_nbd_other	0.178
r_nbd_refined	0.176
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.156
r_mcbond_other	0.119
r_chiral_restr	0.085
r_nbtor_other	0.079
r_xyhbond_nbd_other	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17921
Nucleic Acid Atoms
Solvent Atoms	762
Heterogen Atoms	204

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
AMoRE	phasing