3FBG

Crystal structure of a putative arginate lyase from Staphylococcus haemolyticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	294	100mM Tris HCl pH 8.0, 29% PEG 3350, 200mM magnesium chloride, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.198	α = 90
b = 93.552	β = 98.86
c = 83.24	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	MAR CCD 165 mm		2008-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.6	82.246	99.8	0.096	0.096	8.9	5.2	94084	93896			21.9

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	1.6	1.69	100		0.495	0.495	2.2	5.1	13722

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.6	20	93999	93820	4700	99.81	0.237	0.235	0.275	RANDOM	28.707

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]
2.35		0.42	-0.63		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.3
r_dihedral_angle_4_deg	21.04
r_dihedral_angle_3_deg	13.914
r_dihedral_angle_1_deg	5.843
r_scangle_it	4.181
r_scbond_it	2.607
r_mcangle_it	1.58
r_angle_refined_deg	1.534
r_mcbond_it	0.938
r_chiral_restr	0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.3
r_dihedral_angle_4_deg	21.04
r_dihedral_angle_3_deg	13.914
r_dihedral_angle_1_deg	5.843
r_scangle_it	4.181
r_scbond_it	2.607
r_mcangle_it	1.58
r_angle_refined_deg	1.534
r_mcbond_it	0.938
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5207
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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 R01GM133198.