9QEA | pdb_00009qea

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01839469

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
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.999	α = 90
b = 84.999	β = 90
c = 148.045	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		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

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	2.3	85	92.1	0.117	0.056	0.999	10.7	10		22947			42.38

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	2.3	2.38	99.9		1.218	0.546	0.96	2	11.2

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	2.3	60.176	22880	1144	92.124	0.258	0.2548	0.2588	0.3106	0.3136	72.847

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]
4.03			4.03		-8.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.129
r_dihedral_angle_6_deg	13.713
r_lrange_it	13.53
r_lrange_other	13.529
r_mcangle_it	10.014
r_mcangle_other	10.012
r_scangle_it	9.652
r_scangle_other	9.65
r_dihedral_angle_1_deg	9.136
r_dihedral_angle_2_deg	7.547
r_mcbond_it	6.694
r_mcbond_other	6.687
r_scbond_it	6.272
r_scbond_other	6.271
r_angle_refined_deg	1.653
r_dihedral_angle_other_2_deg	1.48
r_angle_other_deg	0.562
r_symmetry_xyhbond_nbd_refined	0.38
r_nbd_refined	0.236
r_symmetry_nbd_other	0.21
r_xyhbond_nbd_refined	0.204
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.169
r_nbd_other	0.152
r_symmetry_xyhbond_nbd_other	0.114
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
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	11
Heterogen Atoms	30

Software

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