Experiment: 1INL

Crystal Structure of Spermidine Synthase from Thermotoga Maritima

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	300	PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.436	α = 90
b = 197.812	β = 90
c = 51.627	γ = 90

Symmetry
Space Group	P 21 21 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	SBC-2	Double crystal monochromator Si-111	2001-03-28	M	MAD
2	1	x-ray	100	CCD	SBC-2	Double crystal monochromator Si-111	2001-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97925, 0.97938, 0.99187	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.97941	APS	19-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	1.5	50	95.1	0.087	23	4	217343	207448		-3	16

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)
	1.5	1.55	81.4		0.24	4	2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	48.1	207247	207247	10174	95.2	0.199	0.199	0.199	0.2027	0.213	RANDOM	19

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]
-1.22			-1.34		2.56

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.6
c_angle_deg	1.2
c_improper_angle_d	1.07
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9367
Nucleic Acid Atoms
Solvent Atoms	867
Heterogen Atoms

Software

Software
Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
SnB	phasing
SOLVE	phasing
DM	model building
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
DM	phasing