4RMF | pdb_00004rmf

Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	30 % (v/v) pentaerythritol ethoxylate, 0.1 M magnesium formate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.609	α = 90
b = 141.514	β = 90
c = 156.817	γ = 90

Symmetry
Space Group	C 2 2 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	VariMax	2014-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.4	42.04	99.7	0.125	0.125	25.1	16.5	31382	31382			38.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	THROUGHOUT	1C0A	2.4	42.04	29771	29771	1580	99.68	0.2152	0.21671	0.21519	0.21	0.24462	0.24	RANDOM	34.172

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]
0.87			0.4		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.617
r_dihedral_angle_4_deg	21.275
r_dihedral_angle_3_deg	16.821
r_dihedral_angle_1_deg	6.29
r_angle_refined_deg	1.163
r_chiral_restr	0.083
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4323
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.