6J26 | pdb_00006j26

Crystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XNC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Reservoir: 0.015 M tricine pH 8.5, 24%(v/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.17	α = 90
b = 74.17	β = 90
c = 105.934	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2017-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	50	100	26.1	10.1		44104

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	2.07

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	5XNC	2	40.87	41889	2182	99.91	0.19753	0.19603	0.2	0.22769	0.23	RANDOM	32.088

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]
0.01	0.01		0.01		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.659
r_dihedral_angle_3_deg	12.51
r_dihedral_angle_4_deg	12.32
r_dihedral_angle_1_deg	5.626
r_long_range_B_refined	2.162
r_long_range_B_other	2.077
r_angle_refined_deg	1.136
r_scangle_other	0.999
r_mcangle_it	0.942
r_mcangle_other	0.941
r_angle_other_deg	0.873
r_scbond_it	0.572
r_scbond_other	0.572
r_mcbond_it	0.536
r_mcbond_other	0.536
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5712
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Coot	model building
PHASER	phasing