2J3L

Prolyl-tRNA synthetase from Enterococcus faecalis complexed with a prolyl-adenylate analogue ('5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherPRORS FROM RHODOPSEUDOMONAS PALUSTRIS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
152% AMMONIUM SULPHATE, PROLYL-ADENYLATE ANALOGUE
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.44α = 90
b = 121.44β = 90
c = 178.84γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2001-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.33097.70.0811.23.858612
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)
12.32.482.50.432.42.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPRORS FROM RHODOPSEUDOMONAS PALUSTRIS2.3100.556575203797.70.2080.2060.268RANDOM23.29
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]
-0.25-0.250.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.441
r_dihedral_angle_3_deg18.337
r_dihedral_angle_4_deg18.169
r_dihedral_angle_1_deg6.33
r_scangle_it3.133
r_scbond_it1.952
r_angle_refined_deg1.478
r_mcangle_it1.219
r_mcbond_it0.736
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.441
r_dihedral_angle_3_deg18.337
r_dihedral_angle_4_deg18.169
r_dihedral_angle_1_deg6.33
r_scangle_it3.133
r_scbond_it1.952
r_angle_refined_deg1.478
r_mcangle_it1.219
r_mcbond_it0.736
r_nbtor_refined0.303
r_nbd_refined0.204
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.157
r_chiral_restr0.096
r_bond_refined_d0.012
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8959
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing