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)
TypeSourceAccession CodeDetails
experimental modelPDB 4NCX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289Protein 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 coefficientSolvent content
5.1776.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.55α = 90
b = 106.55β = 90
c = 186.16γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.977408ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.95098.40.04623.563.82784827391-368.204
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.98990.5583.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NCX2.946.2372869427357133798.390.19940.19760.2363RANDOM74.425
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]
0.510.250.51-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg17.864
r_dihedral_angle_3_deg16.301
r_dihedral_angle_1_deg6.784
r_mcangle_it3.618
r_mcbond_it2.295
r_mcbond_other2.295
r_angle_refined_deg1.482
r_angle_other_deg0.786
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.236
r_dihedral_angle_4_deg17.864
r_dihedral_angle_3_deg16.301
r_dihedral_angle_1_deg6.784
r_mcangle_it3.618
r_mcbond_it2.295
r_mcbond_other2.295
r_angle_refined_deg1.482
r_angle_other_deg0.786
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3773
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms135

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection