9QDJ | pdb_00009qdj

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911

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
2.23	44.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.701	α = 90
b = 83.701	β = 90
c = 147.691	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+		2018-10-03	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	2.59	46.225	99.7	0.36	0.161	0.988	4.8	11.2		16852			51.64

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	2.71	98.1		2.404	0.808	0.589	0.8	9.6

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	2.597	46.225	16796	843	99.555	0.263	0.2601	0.2617	0.3181	0.3162	64.121

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]
2.824			2.824		-5.648

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.966
r_dihedral_angle_6_deg	14.125
r_lrange_it	9.884
r_lrange_other	9.884
r_dihedral_angle_1_deg	8.254
r_mcangle_it	6.697
r_mcangle_other	6.696
r_scangle_it	6.492
r_scangle_other	6.491
r_dihedral_angle_2_deg	5.653
r_mcbond_it	4.189
r_mcbond_other	4.18
r_scbond_it	4.042
r_scbond_other	4.041
r_angle_refined_deg	1.212
r_angle_other_deg	0.46
r_nbd_refined	0.218
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.176
r_nbd_other	0.166
r_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.066
r_chiral_restr	0.06
r_dihedral_angle_other_2_deg	0.043
r_chiral_restr_other	0.017
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3627
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing