3EFG

Structure of SlyX protein from Xanthomonas campestris pv. campestris str. ATCC 33913

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.1M Tris pH 8.5, 0.2M Ammonium Sulfate, 20% PEG 3350, 4% Glycerol, 1/60 cymotrypsin, then soaked in Na Bromide for phasing, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.945	α = 90
b = 35.945	β = 90
c = 81.82	γ = 120

Symmetry
Space Group	P 63

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 315		2008-02-15	M	MAD
2	1	x-ray		CCD	ADSC QUANTUM 315		2008-04-21	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97931, 0.91966, 0.91948	APS	19-ID

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	1.9	50	99.7	0.051	58.469	12.4	4751	4751		-3	34.9

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)
1,2	1.9	1.94	100		0.533		11.9	298

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	31.13	4065	4065	191	99.71	0.204	0.204	0.204	0.211	RANDOM	38.483

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]
1.62	0.81		1.62		-2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.401
r_dihedral_angle_3_deg	18.643
r_dihedral_angle_4_deg	13.087
r_scangle_it	5.167
r_dihedral_angle_1_deg	3.83
r_scbond_it	2.939
r_mcangle_it	1.872
r_angle_refined_deg	1.389
r_angle_other_deg	0.901
r_mcbond_it	0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.401
r_dihedral_angle_3_deg	18.643
r_dihedral_angle_4_deg	13.087
r_scangle_it	5.167
r_dihedral_angle_1_deg	3.83
r_scbond_it	2.939
r_mcangle_it	1.872
r_angle_refined_deg	1.389
r_angle_other_deg	0.901
r_mcbond_it	0.88
r_mcbond_other	0.155
r_chiral_restr	0.063
r_bond_refined_d	0.017
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	404
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.