4KNA

Crystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	31 mg/mL ButhA.00020.d.B1.PS01757 against Morpheus screen condition A10: 10% PEG8000, 20% ethylene glycol, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma, pH 8.5, crystal tracking ID 243761a10, unique puck ID pna1-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.05	α = 90
b = 120.69	β = 107.36
c = 53.91	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX-300		2013-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07811	APS	21-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	1.95	50	99.8	0.09	13.09	6.3	75602	75481		-3	32.62

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	1.95	2	99.8		0.514	3.44	6.3

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	1.95	49.26	75480	3800	99.97	0.1544	0.1524	0.1921	RANDOM	29.1039

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]
-0.09		-1.04	-1.12		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	21.391
r_dihedral_angle_3_deg	11.959
r_dihedral_angle_1_deg	5.808
r_mcangle_it	1.669
r_angle_refined_deg	1.446
r_mcbond_it	1.125
r_mcbond_other	1.125
r_angle_other_deg	0.801
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	21.391
r_dihedral_angle_3_deg	11.959
r_dihedral_angle_1_deg	5.808
r_mcangle_it	1.669
r_angle_refined_deg	1.446
r_mcbond_it	1.125
r_mcbond_other	1.125
r_angle_other_deg	0.801
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7230
Nucleic Acid Atoms
Solvent Atoms	866
Heterogen Atoms	20

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.