2I4N

Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with CysAMS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M citric acid (pH 5.5), 10-11 % PEG 3000, 15-20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 217.9α = 90
b = 107.47β = 120.43
c = 110.66γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.97935ESRFID14-1

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
12.855093.50.012.551737483772.852.85
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)
12.85375.50.4111.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.855173746284251494.620.214360.210980.27676RANDOM59.182
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]
-2.57-0.680.31.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.992
r_dihedral_angle_3_deg20.632
r_dihedral_angle_4_deg17.924
r_dihedral_angle_1_deg6.975
r_scangle_it2.32
r_angle_refined_deg1.531
r_scbond_it1.383
r_mcangle_it1.11
r_mcbond_it0.635
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.992
r_dihedral_angle_3_deg20.632
r_dihedral_angle_4_deg17.924
r_dihedral_angle_1_deg6.975
r_scangle_it2.32
r_angle_refined_deg1.531
r_scbond_it1.383
r_mcangle_it1.11
r_mcbond_it0.635
r_nbtor_refined0.318
r_symmetry_hbond_refined0.308
r_nbd_refined0.243
r_symmetry_vdw_refined0.196
r_xyhbond_nbd_refined0.173
r_chiral_restr0.097
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_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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10507
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing