6CY6 | pdb_00006cy6

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Escherichia coli in complex with tris(hydroxymethyl)aminomethane.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R9M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2 M Ammonium phosphate monobasic, 0.1 M Tris, 50% v/v MPD

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.499	α = 90
b = 107.499	β = 90
c = 65.021	γ = 120

Symmetry
Space Group	P 6 2 2

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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2016-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.75	30	100	0.048	0.048	51.1	12.8		22903

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	1.75	1.78	100		0.65	4.3	13

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	4R9M	1.75	93.1	21759	1144	99.88	0.15587	0.15352	0.17	0.20067	0.21	RANDOM	31.44

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]
-0.32	-0.16		-0.32		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.246
r_dihedral_angle_4_deg	20.06
r_dihedral_angle_3_deg	11.266
r_long_range_B_refined	7.607
r_long_range_B_other	7.526
r_scangle_other	6.204
r_scbond_it	4.317
r_scbond_other	4.28
r_dihedral_angle_1_deg	4.025
r_mcangle_it	3.148
r_mcangle_other	3.146
r_mcbond_it	2.237
r_mcbond_other	2.225
r_angle_refined_deg	2.098
r_angle_other_deg	1.005
r_chiral_restr	0.132
r_gen_planes_refined	0.025
r_bond_refined_d	0.021
r_gen_planes_other	0.019
r_bond_other_d	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	1422
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data scaling
HKL-3000	data reduction
Coot	model building
PHASER	phasing