2FN1

Crystal structures of Yersinia enterocolitica salicylate synthase (Irp9) in complex with the reaction products salicylate and pyruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QDL	composite search probe from 1QDL, 1I7Q and 1I1Q
experimental model	PDB	1I7Q	composite search probe from 1QDL, 1I7Q and 1I1Q
experimental model	PDB	1I1Q	composite search probe from 1QDL, 1I7Q and 1I1Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.571	α = 90
b = 145.298	β = 108.39
c = 58.86	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	Rigaku Max Flux mirrors	2005-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	30	94	0.049	0.049	20.7	4.8	52602	49446	2.5	2.5	33.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	88.7		0.299	0.299		4.7	3453

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	composite search probe from 1QDL, 1I7Q and 1I1Q	2.1	27.37	46901	46901	2513	93.62	0.19091	0.19091	0.18803	0.24516	RANDOM	33.63

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]
-0.07		-0.1	0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.635
r_dihedral_angle_4_deg	16.422
r_dihedral_angle_3_deg	14.004
r_dihedral_angle_1_deg	6.61
r_scangle_it	5.39
r_mcangle_it	4.154
r_scbond_it	4.008
r_mcbond_it	3.335
r_angle_refined_deg	1.527
r_nbtor_refined	0.301
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.161
r_chiral_restr	0.097
r_metal_ion_refined	0.045
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6241
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
SCALEPACK	data scaling
AMoRE	phasing