3RET | pdb_00003ret

Salicylate and Pyruvate Bound Structure of the Isochorismate-Pyruvate Lyase K42E Mutant from Pseudomonas aerugionsa

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	3.6	298	0.004 M gly-gly, 0.100 M sodium acetate, 12% glycerol, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.144	α = 90
b = 57.313	β = 90
c = 60.334	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	MARMOSAIC 325 mm CCD	Rh coated flat mirror, toroidal focusing mirror	2009-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0000	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.79	25.89	97.2	0.098	5.7	3.5	15734	13690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.84	97.9		0.375	2	3.3	2186

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	PDB ENTRY 2H9D	1.79	25.89	15294	13690	1532	97.34	0.21357	0.21357	0.20793	0.21	0.26403	0.26	RANDOM	20.854

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.415
r_dihedral_angle_4_deg	16.521
r_dihedral_angle_3_deg	14.738
r_scangle_it	5.526
r_dihedral_angle_1_deg	5.158
r_scbond_it	3.446
r_mcangle_it	2.055
r_angle_refined_deg	1.874
r_mcbond_it	1.238
r_chiral_restr	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.415
r_dihedral_angle_4_deg	16.521
r_dihedral_angle_3_deg	14.738
r_scangle_it	5.526
r_dihedral_angle_1_deg	5.158
r_scbond_it	3.446
r_mcangle_it	2.055
r_angle_refined_deg	1.874
r_mcbond_it	1.238
r_chiral_restr	0.14
r_bond_refined_d	0.022
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1519
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	32

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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.