8W9I

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UCM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	0.2 M ammonium acetate, 0.1 M BIS-TRIS, 26% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.584	α = 90
b = 102.622	β = 90
c = 194.084	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2019-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.987	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.35	97.05	99	0.126	0.963	12.6	6.4		55512

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.39	89.2		0.911

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	49.656	55512	2791	99.795	0.216	0.2141	0.2484	39.717

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]
1.739			-1.726		-0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.874
r_dihedral_angle_3_deg	12.739
r_dihedral_angle_1_deg	6.349
r_lrange_it	3.399
r_lrange_other	3.399
r_dihedral_angle_2_deg	3.364
r_mcangle_it	2.166
r_mcangle_other	2.166
r_scangle_it	2.002
r_scangle_other	2.002
r_mcbond_it	1.258
r_mcbond_other	1.257
r_scbond_it	1.131
r_scbond_other	1.131
r_angle_refined_deg	0.811
r_angle_other_deg	0.289
r_symmetry_nbd_other	0.19
r_nbd_refined	0.186
r_nbtor_refined	0.167
r_nbd_other	0.166
r_symmetry_nbd_refined	0.107
r_xyhbond_nbd_refined	0.105
r_symmetry_xyhbond_nbd_other	0.078
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_refined	0.076
r_chiral_restr	0.038
r_chiral_restr_other	0.006
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8652
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
MOLREP	phasing