2X5X

The crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolution reveals details of the active site and suggests a substrate binding mode

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	PHAZ7 WAS CRYSTALLIZED IN THE PRESENCE OF PMSF USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 16 C. THE WELL SOLUTION CONSISTED OF 20% W/V PEG3350 AND 0.2 M NA IODIDE AND A 0.1 M PMSF STOCK SOLUTION IN ISOPROPANOL WAS ADDED TO THE WELL TO A FINAL CONCENTRATION OF 10 MM.A 1.5 MICROLITER PROTEIN SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION ON SILICONIZED COVERSLIPS.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.63	α = 90
b = 140.58	β = 90
c = 56.75	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	ADSC CCD		2008-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.2	20	99.9	0.1	11.1	5.9		124737		3.5

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	1.2	1.23	99.9		0.43	3.6	99.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FREE R-VALUE	PDB ENTRY 2VTV	1.2	20	98593		95	0.1392	0.139		0.176	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
16		3140

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.519
s_approx_iso_adps	0.091
s_non_zero_chiral_vol	0.077
s_zero_chiral_vol	0.073
s_similar_adp_cmpnt	0.033
s_from_restr_planes	0.0286
s_angle_d	0.026
s_bond_d	0.011
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2549
Nucleic Acid Atoms
Solvent Atoms	563
Heterogen Atoms	29

Software

Software
Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
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.