4WYF | pdb_00004wyf

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a DSF fragment hit

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	25 mM HEPES pH 7.5, 50 mM NaCl, 0.1 mM TCEP Reservoir:9% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES pH 7.5 Cryo: 15% PEG 400 in reservoir solution

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.086	α = 90
b = 66.092	β = 90
c = 203.194	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	PIXEL	DECTRIS PILATUS 6M		2012-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	2.25	101.06	98.5	0.088	15.4	4.9		38797

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.25	101.06	38797	2065	98.46	0.1903	0.1879	0.1873	0.2357	0.2349	RANDOM	14.437

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]
-0.62			-0.8		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.21
r_dihedral_angle_4_deg	16.062
r_dihedral_angle_3_deg	14.417
r_dihedral_angle_1_deg	5.846
r_angle_refined_deg	1.318
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6395
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
PDB_EXTRACT	data extraction

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.