2J3M

PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J3LPDB ENTRY 2J3L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 6000, 1M LICL, 100MM MES, PH 6.5, 5MM PROLINOL, 2MM ATP, 6MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.583α = 90
b = 92.679β = 106.11
c = 101.223γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-04-30MSINGLE 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
12.330990.16.443.754112
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)
12.32.498.60.451.953.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2J3L2.329.495221318941000.1980.1960.26RANDOM21.84
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]
-0.030.47-0.260.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_4_deg19.849
r_dihedral_angle_3_deg16.968
r_dihedral_angle_1_deg7.073
r_scangle_it3.679
r_scbond_it2.33
r_angle_refined_deg1.694
r_mcangle_it1.359
r_mcbond_it0.828
r_symmetry_hbond_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_4_deg19.849
r_dihedral_angle_3_deg16.968
r_dihedral_angle_1_deg7.073
r_scangle_it3.679
r_scbond_it2.33
r_angle_refined_deg1.694
r_mcangle_it1.359
r_mcbond_it0.828
r_symmetry_hbond_refined0.341
r_nbtor_refined0.316
r_symmetry_vdw_refined0.241
r_nbd_refined0.232
r_xyhbond_nbd_refined0.19
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms8791
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing