3UND | pdb_00003und

Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TMQ	PDB ENTRY 3tmq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	EBS internal tracking number 227318B6, from a focus screen based on PACT F12. 0.2 M malonate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, 10 mM D-arabinose-5-phosphate, 10 mM phosphoenolpyruvate, vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.32	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.84	α = 90
b = 146.24	β = 90
c = 178.94	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	RIGAKU SATURN 944+		2011-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

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	50	97.3	0.08	19.54	5.6		71084		-3	27.104

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	2.15	94.2		0.376	4.4	4.8

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	MR	THROUGHOUT	PDB ENTRY 3tmq	2.1	50	71015	3581	97.34	0.168	0.167	0.17	0.192	0.2	RANDOM	24.112

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]
0.77			-1.79		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.598
r_dihedral_angle_4_deg	18.461
r_dihedral_angle_3_deg	12.189
r_dihedral_angle_1_deg	6.072
r_angle_refined_deg	1.593
r_angle_other_deg	1.233
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.598
r_dihedral_angle_4_deg	18.461
r_dihedral_angle_3_deg	12.189
r_dihedral_angle_1_deg	6.072
r_angle_refined_deg	1.593
r_angle_other_deg	1.233
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8444
Nucleic Acid Atoms
Solvent Atoms	696
Heterogen Atoms	204

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 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.