3TMQ | pdb_00003tmq

Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei in complex with D-arabinose-5-phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	Internal tracking number224822. PACT screen F5. 0.2M Sodium nitrate, 0.1M BIS-TRIS propane, 20% PEG3350, protein drop contains 10mM D-arabinose-5-phosphate. BupsA.00102a.A1 PS00621 30.3mg/ml., pH 6.5, vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.72	α = 90
b = 92.08	β = 90
c = 152.98	γ = 90

Symmetry
Space Group	P 21 21 21

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		2011-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	49.2	98	0.106	13.87	5.32	80219	78647		-3	26.74

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	87.7		0.553	3.1	4.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3SZ8	2.1	49.2	73746	3679	98.84	0.181	0.179	0.18	0.217	0.22	RANDOM	20.633

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]
-0.74			2.19		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.557
r_dihedral_angle_4_deg	18.216
r_dihedral_angle_3_deg	11.906
r_dihedral_angle_1_deg	5.918
r_angle_refined_deg	1.415
r_angle_other_deg	1.122
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.557
r_dihedral_angle_4_deg	18.216
r_dihedral_angle_3_deg	11.906
r_dihedral_angle_1_deg	5.918
r_angle_refined_deg	1.415
r_angle_other_deg	1.122
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8044
Nucleic Acid Atoms
Solvent Atoms	629
Heterogen Atoms	88

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MD2	data collection
XDS	data reduction

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.