3HGX

Crystal Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase K42A mutant in complex with salicylate and pyruvate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H9D	PDB ENTRY 2H9D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291.15	0.1M Tris-HCl, pH 8.5, 2M ammonium phosphate, 13% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.015	α = 90
b = 53.15	β = 90
c = 82.336	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113.15	IMAGE PLATE	RIGAKU RAXIS IV++		2007-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.5	100	99.9	0.101	15.234	6.6		7706

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)
	2.5	2.59	99.9		0.277		6.7	749

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H9D	2.5	41.49	7346	350	99.75	0.218	0.216	0.276	RANDOM	15.597

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			-0.01		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.461
r_dihedral_angle_3_deg	15.732
r_dihedral_angle_4_deg	13.846
r_dihedral_angle_1_deg	4.613
r_scangle_it	1.879
r_angle_refined_deg	1.219
r_scbond_it	1.2
r_mcangle_it	0.813
r_mcbond_it	0.5
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.461
r_dihedral_angle_3_deg	15.732
r_dihedral_angle_4_deg	13.846
r_dihedral_angle_1_deg	4.613
r_scangle_it	1.879
r_angle_refined_deg	1.219
r_scbond_it	1.2
r_mcangle_it	0.813
r_mcbond_it	0.5
r_nbtor_refined	0.299
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.094
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1578
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.