3SZ8

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	EBS internal tracking number 223672H7. PACT H7. 0.2 M Na acetate, 0.1 M Bis Tris propane pH 8.5, 20% PEG 3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.49	α = 90
b = 83.32	β = 116.59
c = 87.87	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	MARMOSAIC 300 mm CCD		2011-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03317	APS	23-ID-D

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	2.05	50	99.2	0.067	13.62	3.6		68845		-3	33.651

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	2.05	2.1	99.1		0.47	2.6	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2.05	43.81	68771	3483	99.29	0.185	0.183	0.221	RANDOM	26.294

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]
0.34		0.9	0.22		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.004
r_dihedral_angle_4_deg	15.22
r_dihedral_angle_3_deg	13.085
r_dihedral_angle_1_deg	5.765
r_scangle_it	3.62
r_scbond_it	2.176
r_angle_refined_deg	1.417
r_mcangle_it	1.324
r_angle_other_deg	0.933
r_mcbond_it	0.722

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.004
r_dihedral_angle_4_deg	15.22
r_dihedral_angle_3_deg	13.085
r_dihedral_angle_1_deg	5.765
r_scangle_it	3.62
r_scbond_it	2.176
r_angle_refined_deg	1.417
r_mcangle_it	1.324
r_angle_other_deg	0.933
r_mcbond_it	0.722
r_mcbond_other	0.176
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7789
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	16

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.