2FPC

Structure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Native structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	295	0.8M potassium sodium tartrate tetrahydrate, 100mM HEPES-Na, 2mM secologanin, pH 7.5, VAPOR DIFFUSION, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.607	α = 90
b = 148.607	β = 90
c = 121.069	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH	double crystal Si[111]	2005-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8057	EMBL/DESY, HAMBURG	X11

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	3	20	96	0.122		11.8	19913	19104	2	2	50

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	3	3.04	95		0.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Native structure	3	20	2	19913	19104	787	100	0.193	0.1882	0.18606	0.24	RANDOM	27.566

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]
4.62	2.31		4.62		-6.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.145
r_scangle_it	5.524
r_scbond_it	3.464
r_angle_refined_deg	1.833
r_mcangle_it	1.346
r_mcbond_it	0.685
r_symmetry_vdw_refined	0.273
r_nbd_refined	0.256
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.118
r_symmetry_hbond_refined	0.104
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4764
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MOLREP	phasing