2X76 | pdb_00002x76

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	2X5X	PDB ENTRY 2X5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	PHAZ7 WAS CRYSTALLIZED 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. A 1.5 MICROLITRES PROTEIN SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION ON SILICONIZED COVERSLIPS.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.24

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 QUANTUM 4		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	1.45	20	99.9	0.1	13.1	5.9		71446		3.9

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	1.45	1.49	99.8		0.43	4.1	5.95

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIRECT METHODS	FREE R-VALUE	PDB ENTRY 2X5X	1.45	20	67830		94.4	0.1345		0.13	0.178	0.17	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
14		3040.5

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.497
s_approx_iso_adps	0.083
s_non_zero_chiral_vol	0.056
s_zero_chiral_vol	0.053
s_similar_adp_cmpnt	0.036
s_from_restr_planes	0.0274
s_angle_d	0.027
s_bond_d	0.011
s_rigid_bond_adp_cmpnt	0.003
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2549
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	22

Software

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