2I4O

Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthernative R. palustris Prolyl-tRNA synthetase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M hepes (pH 7.0), 8-10 % PEG 8K, 5-10 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8957.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.2α = 90
b = 211.21β = 90
c = 148.21γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.42093.60.0086470163656562.42.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5593.70.4743.7

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 REPLACEMENTTHROUGHOUTnative R. palustris Prolyl-tRNA synthetase2.47016363935339795.970.200510.197350.26104RANDOM36.851
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]
1.48-2.30.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.209
r_dihedral_angle_4_deg19.099
r_dihedral_angle_3_deg17.307
r_dihedral_angle_1_deg6.524
r_scangle_it2.72
r_scbond_it1.761
r_angle_refined_deg1.566
r_mcangle_it1.227
r_mcbond_it0.711
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.209
r_dihedral_angle_4_deg19.099
r_dihedral_angle_3_deg17.307
r_dihedral_angle_1_deg6.524
r_scangle_it2.72
r_scbond_it1.761
r_angle_refined_deg1.566
r_mcangle_it1.227
r_mcbond_it0.711
r_nbtor_refined0.303
r_symmetry_vdw_refined0.214
r_nbd_refined0.212
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.171
r_chiral_restr0.098
r_metal_ion_refined0.039
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10485
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing