9QC4 | pdb_00009qc4

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QI8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	reservoir: 0.25 M NaOAc, 14% W/V PEG 3350 Protein buffer: 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.983	α = 90
b = 83.983	β = 90
c = 147.324	γ = 90

Symmetry
Space Group	P 41 21 2

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+		2019-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.6	46.275	99.7	0.158	0.062	0.988	8.5	13.8		16862			33.02

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72	97.5		0.522	0.222	0.972	2.3	11.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.601	46.275	16807	841	99.638	0.235	0.2318	0.2344	0.2921	0.2916	55.198

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]
2.976			2.976		-5.952

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.54
r_dihedral_angle_6_deg	12.665
r_dihedral_angle_1_deg	7.293
r_lrange_it	7.016
r_lrange_other	7.011
r_dihedral_angle_2_deg	5.181
r_mcangle_it	4.656
r_mcangle_other	4.656
r_scangle_it	4.387
r_scangle_other	4.386
r_mcbond_it	2.882
r_mcbond_other	2.87
r_scbond_it	2.611
r_scbond_other	2.611
r_angle_refined_deg	1.102
r_dihedral_angle_other_2_deg	0.506
r_angle_other_deg	0.413
r_symmetry_nbd_other	0.2
r_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.172
r_nbd_other	0.163
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.061
r_chiral_restr	0.051
r_chiral_restr_other	0.027
r_bond_other_d	0.007
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3551
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building