5XBY | pdb_00005xby

Crystal structure of the PKA-Protein A fusion protein (end-to-end fusion)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IZX	2IZX, 4ZNC
experimental model	PDB	4ZNC	2IZX, 4ZNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	296	100mM Tris pH 8.5, 2.16M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.988	α = 90
b = 174.147	β = 90
c = 103.611	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 315r		2017-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	3.25	50	98.9	23.6	6.3		10889

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	3.3	3.42

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	2IZX, 4ZNC	3.25	43.537	10339	541	97.19	0.25359	0.25076	0.25	0.30675	0.31	RANDOM	165.823

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]
3.46			-11.1		7.64

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	39.619
r_dihedral_angle_2_deg	37.184
r_dihedral_angle_4_deg	24.829
r_long_range_B_refined	18.646
r_dihedral_angle_3_deg	18.308
r_mcangle_it	13.676
r_scbond_it	13.055
r_mcbond_it	9.862
r_dihedral_angle_1_deg	4.965
r_rigid_bond_restr	3.02
r_angle_refined_deg	1.729
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
r_long_range_B_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2553
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing