4HVC

Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	303	20% PEG 3350, 0.6 M CaCl2, 50 mM HEPES , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.544	α = 90
b = 93.1	β = 107.95
c = 87.004	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	173	CCD	ADSC QUANTUM 315		2012-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.000	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	50					73215

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	98.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	46.43	69440	3678	98.48	0.20498	0.20379	0.22725	RANDOM	49.541

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]
-1.55		0.03	0.96		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.588
r_dihedral_angle_4_deg	15.802
r_dihedral_angle_3_deg	14.044
r_dihedral_angle_1_deg	5.461
r_scangle_it	1.862
r_scbond_it	1.134
r_angle_refined_deg	1.065
r_mcangle_it	0.669
r_mcbond_it	0.344
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.588
r_dihedral_angle_4_deg	15.802
r_dihedral_angle_3_deg	14.044
r_dihedral_angle_1_deg	5.461
r_scangle_it	1.862
r_scbond_it	1.134
r_angle_refined_deg	1.065
r_mcangle_it	0.669
r_mcbond_it	0.344
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7610
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	114

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.