2FN0 | pdb_00002fn0

Crystal structure of Yersinia enterocolitica salicylate synthase (Irp9)

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
2.39	48.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.74	α = 90
b = 145.671	β = 107.97
c = 58.807	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	CCD	ADSC QUANTUM 4		2005-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	1.85	30	93.9	0.048	0.048	16.1	3.8	77309	72593	2.5	2.5	26.7

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)
	1.85	1.89	87.5		0.306	0.306		3.8	5176

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	composite search probe from 1QDL, 1I7Q and 1I1Q	1.85	28.17	73421	68906	3649	93.85	0.18988	0.18988	0.18717	0.19	0.24035	0.19	RANDOM	30.577

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]
-0.03		-0.03	0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.796
r_dihedral_angle_4_deg	16.432
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_1_deg	6.411
r_scangle_it	5.29
r_mcangle_it	4.08
r_scbond_it	3.839
r_mcbond_it	3.261
r_angle_refined_deg	1.506
r_nbtor_refined	0.303
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.106
r_metal_ion_refined	0.07
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6318
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
X-GEN	data reduction
SCALEPACK	data scaling
AMoRE	phasing