9QBR | pdb_00009qbr

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01991231

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, 500 mM NaCl, 5% GLYCEROL, 2 mM DTT, PH 7.0,

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.589	α = 90
b = 83.589	β = 90
c = 147.406	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	PIXEL	DECTRIS PILATUS 6M		2019-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.4	147.41	100	0.254	0.272	0.097	0.997	6.5	14.4		21202			57.9

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	2.4	2.49	100		5.109	2.014	0.597	0.7	14.1

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	2.4	72.712	21130	1067	99.915	0.237	0.2331	0.2355	0.3081	0.3082	77.859

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]
4.51			4.51		-9.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.381
r_dihedral_angle_6_deg	13.426
r_lrange_other	10.73
r_lrange_it	10.728
r_dihedral_angle_1_deg	8.342
r_mcangle_it	7.894
r_mcangle_other	7.892
r_scangle_it	7.33
r_scangle_other	7.328
r_dihedral_angle_2_deg	6.02
r_mcbond_it	5.056
r_mcbond_other	5.045
r_scbond_it	4.595
r_scbond_other	4.594
r_angle_refined_deg	1.371
r_angle_other_deg	0.487
r_dihedral_angle_other_2_deg	0.385
r_symmetry_nbd_other	0.212
r_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.174
r_nbd_other	0.168
r_symmetry_nbd_refined	0.127
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.063
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	3556
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing