5FOG | pdb_00005fog

Crystal structure of hte Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of norvaline (Nv2AA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WFGPDB ENTRY 2WFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.90.1 M KNO3 PH 6.9, 22% (W/V) PEG 3350. 20 % ETHYLENE GLYCOL AS CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
3.463

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.73α = 90
b = 107.73β = 90
c = 309.51γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.315990.1168.1818172
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)
12.32.36981.21.97.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WFG2.3101.7677686401499.740.202610.200870.210.236070.24RANDOM46.977
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]
0.910.911.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.972
r_dihedral_angle_3_deg14.495
r_dihedral_angle_4_deg12.164
r_long_range_B_refined6.744
r_long_range_B_other6.744
r_dihedral_angle_1_deg6.241
r_scangle_other4.633
r_mcangle_it3.891
r_mcangle_other3.891
r_scbond_it2.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.972
r_dihedral_angle_3_deg14.495
r_dihedral_angle_4_deg12.164
r_long_range_B_refined6.744
r_long_range_B_other6.744
r_dihedral_angle_1_deg6.241
r_scangle_other4.633
r_mcangle_it3.891
r_mcangle_other3.891
r_scbond_it2.783
r_scbond_other2.783
r_mcbond_it2.351
r_mcbond_other2.351
r_angle_refined_deg1.382
r_angle_other_deg0.893
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms8891
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing