9QC3 | pdb_00009qc3

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593

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
2.22	44.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.669	α = 90
b = 83.669	β = 90
c = 147.261	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		2019-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91188	Diamond	I04-1

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	2.28	147.26	100	0.142	0.043	0.991	11.1	12.7		24663

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	2.28	2.32	100		1.702	0.495	0.894	0.9	12.8

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	2.28	72.853	24587	1232	99.951	0.217	0.214	0.2168	0.2769	0.2765	66.897

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]
2.656			2.656		-5.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.473
r_dihedral_angle_6_deg	14.122
r_lrange_it	10.224
r_lrange_other	10.223
r_dihedral_angle_1_deg	7.746
r_scangle_it	7.692
r_scangle_other	7.69
r_mcangle_it	7.447
r_mcangle_other	7.445
r_dihedral_angle_2_deg	5.244
r_mcbond_it	4.975
r_mcbond_other	4.974
r_scbond_other	4.97
r_scbond_it	4.968
r_angle_refined_deg	1.379
r_dihedral_angle_other_2_deg	0.854
r_angle_other_deg	0.501
r_symmetry_xyhbond_nbd_refined	0.299
r_symmetry_nbd_other	0.209
r_nbd_refined	0.204
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.16
r_symmetry_nbd_refined	0.112
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3591
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	31

Software

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