5BMU

The crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BVX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.4293.15Ammonium sulfate, Sodium chloride, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.9458.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.063α = 90
b = 92.063β = 90
c = 185.948γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9796PAL/PLS5C (4A)

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
12.6501000.15716.55.453953-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.691002.85

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 REPLACEMENTTHROUGHOUT4BVX2.648.9351915198099.780.139170.138010.16957RANDOM31.298
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]
0.070.07-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.531
r_dihedral_angle_4_deg23.609
r_dihedral_angle_3_deg18.165
r_dihedral_angle_1_deg7.734
r_long_range_B_refined4.998
r_long_range_B_other4.998
r_mcangle_it3.442
r_mcangle_other3.442
r_scangle_other2.218
r_mcbond_it2.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.531
r_dihedral_angle_4_deg23.609
r_dihedral_angle_3_deg18.165
r_dihedral_angle_1_deg7.734
r_long_range_B_refined4.998
r_long_range_B_other4.998
r_mcangle_it3.442
r_mcangle_other3.442
r_scangle_other2.218
r_mcbond_it2.015
r_mcbond_other2.013
r_angle_refined_deg1.538
r_scbond_it1.313
r_scbond_other1.313
r_angle_other_deg1.049
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10457
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building