4NCX

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum 3D7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HVCPDB entry 4HVC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289Morpheus(b2): 0.1M each MES, Imidazole, pH 6.5, 0.09M each NaF, NaBr, NaI, 30% ethylene glycol, PEG-8000 and 5mM L-Proline, 5mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.96α = 90
b = 91.38β = 129.48
c = 110.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2013-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9786APS21-ID-F

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
11.855099.20.04919.364.59746196638-332.393
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)
11.851.999.20.4913.11

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 REPLACEMENTTHROUGHOUTPDB entry 4HVC1.8546.4610146996637483299.520.17090.1690.2064RANDOM33.037
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]
0.850.320.39-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.708
r_dihedral_angle_4_deg20.676
r_dihedral_angle_3_deg12.711
r_dihedral_angle_1_deg6.52
r_mcangle_it2.243
r_angle_refined_deg1.511
r_mcbond_it1.44
r_mcbond_other1.437
r_angle_other_deg0.833
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.708
r_dihedral_angle_4_deg20.676
r_dihedral_angle_3_deg12.711
r_dihedral_angle_1_deg6.52
r_mcangle_it2.243
r_angle_refined_deg1.511
r_mcbond_it1.44
r_mcbond_other1.437
r_angle_other_deg0.833
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7084
Nucleic Acid Atoms
Solvent Atoms604
Heterogen Atoms27

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction