8YTK | pdb_00008ytk

Crystal structure of human prolyl-tRNA synthetase in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HVC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	289	0.2 M magnesium chloride, 0.1 M Tris pH 8.4, 20% PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.602	α = 90
b = 92.157	β = 108.629
c = 86.621	γ = 90

Symmetry
Space Group	P 1 21 1

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		2021-10-17	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	2.55	50	99.6	0.195	0.975	26.4	3.4		34745

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	99.4		0.119	0.975	7.85	3.6

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	2.553	46.121	34607	1797	99.46	0.205	0.2023	0.2043	0.2496	0.2504	44.659

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]
-1.265		-0.9	3.652		-1.451

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.784
r_dihedral_angle_6_deg	14.673
r_dihedral_angle_1_deg	5.82
r_dihedral_angle_2_deg	3.855
r_lrange_it	2.234
r_lrange_other	2.234
r_angle_refined_deg	1.067
r_scangle_it	0.942
r_scangle_other	0.942
r_mcangle_it	0.862
r_mcangle_other	0.862
r_scbond_it	0.56
r_scbond_other	0.56
r_mcbond_it	0.503
r_mcbond_other	0.503
r_angle_other_deg	0.41
r_symmetry_nbd_other	0.201
r_nbd_refined	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.165
r_nbd_other	0.157
r_symmetry_nbd_refined	0.104
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_refined	0.058
r_chiral_restr	0.055
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	7362
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	68

Software

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