4G8T | pdb_00004g8t

Crystal structure of a glucarate dehydratase related protein, from actinobacillus succinogenes, target EFI-502312, with sodium and sulfate bound, ordered loop

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EC7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffuction	7.5	298	Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.2 M Lithium Sulfate, 0.1 M Sodium Acetate, 0.1 M HEPES, 25% PEG4000); Cryoprotection (Reservoir, + 20% glycerol and 50 mM MgCl), sitting drop vapor diffuction, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.837	α = 90
b = 124.854	β = 90
c = 139.093	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	RAYONIX MX225HE	MIRRORS	2012-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	139.093	99.7	0.112	0.112	9.2	6.9	210738	210738

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	99.1		0.531	0.531	1.4	6.4	30329

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1EC7	1.7	28.477	210083	210083	10561	99.4	0.1535	0.1535	0.1521	0.1504	0.1791	0.1774	RANDOM	22.9951

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]
9.727			-2.7479		-6.979

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.929
f_angle_d	1.005
f_chiral_restr	0.071
f_bond_d	0.011
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13696
Nucleic Acid Atoms
Solvent Atoms	1973
Heterogen Atoms	98

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

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.