8W8L

Crystal structure of bacterial prolyl-tRNA synthetase in complex with inhibitor PAA-38

X-RAY DIFFRACTION

---

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 sulfate, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.484	α = 90
b = 103.06	β = 90
c = 194.095	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		2023-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9785	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.82	97.05	99.1	0.056	0.061	0.999	20.3	6.1		132338

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.92			0.448	0.51	0.866	2.7

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	1.824	97.048	132241	6624	99.022	0.213	0.2112	0.2412	25.033

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]
2.09			-1.029		-1.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.278
r_dihedral_angle_3_deg	13.588
r_dihedral_angle_1_deg	6.473
r_dihedral_angle_2_deg	4.049
r_lrange_it	3.51
r_lrange_other	3.393
r_scangle_it	1.857
r_scangle_other	1.857
r_mcangle_it	1.725
r_mcangle_other	1.725
r_scbond_it	1.104
r_scbond_other	1.104
r_angle_refined_deg	1.047
r_mcbond_it	1.032
r_mcbond_other	1.031
r_angle_other_deg	0.376
r_symmetry_nbd_other	0.201
r_nbd_refined	0.197
r_nbd_other	0.183
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.126
r_symmetry_nbd_refined	0.09
r_symmetry_nbtor_other	0.079
r_chiral_restr_other	0.072
r_chiral_restr	0.049
r_symmetry_xyhbond_nbd_other	0.03
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8681
Nucleic Acid Atoms
Solvent Atoms	807
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing