4OLF

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
5.17	76.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.55	α = 90
b = 106.55	β = 90
c = 186.16	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC QUANTUM 315r		2014-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.9	50	98.4	0.046	23.56	3.8	27848	27391		-3	68.204

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	2.9	2.98	99		0.558	3.13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	4NCX	2.9	46.237	28694	27357	1337	98.39	0.1994	0.1976	0.2363	RANDOM	74.425

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]
0.51	0.25		0.51		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.236
r_dihedral_angle_4_deg	17.864
r_dihedral_angle_3_deg	16.301
r_dihedral_angle_1_deg	6.784
r_mcangle_it	3.618
r_mcbond_it	2.295
r_mcbond_other	2.295
r_angle_refined_deg	1.482
r_angle_other_deg	0.786
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.236
r_dihedral_angle_4_deg	17.864
r_dihedral_angle_3_deg	16.301
r_dihedral_angle_1_deg	6.784
r_mcangle_it	3.618
r_mcbond_it	2.295
r_mcbond_other	2.295
r_angle_refined_deg	1.482
r_angle_other_deg	0.786
r_chiral_restr	0.074
r_bond_refined_d	0.011
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	3773
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	135

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection

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 R01GM157729.