5FOL | pdb_00005fol

Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with a post-transfer editing analogue of isoeucine (Ile2AA)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.51.4 M SODIUM/POTASSIUM PHOSPHATE PH 5.5. 20% GLYCEROL WAS USED AS CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
2.654

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.957α = 90
b = 64.957β = 90
c = 167.292γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17USSRFBL17U

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
11.7750990.1531.214.6253162
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)
11.771.81395.30.24518.6

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 2WFG1.7735.4429524157386.370.19780.1960.20.232250.23RANDOM24.742
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]
0.270.27-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.737
r_dihedral_angle_3_deg14.47
r_dihedral_angle_4_deg14.157
r_long_range_B_refined6.628
r_dihedral_angle_1_deg6.458
r_long_range_B_other6.404
r_scangle_other4.153
r_mcangle_it2.756
r_mcangle_other2.755
r_scbond_it2.652
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.737
r_dihedral_angle_3_deg14.47
r_dihedral_angle_4_deg14.157
r_long_range_B_refined6.628
r_dihedral_angle_1_deg6.458
r_long_range_B_other6.404
r_scangle_other4.153
r_mcangle_it2.756
r_mcangle_other2.755
r_scbond_it2.652
r_scbond_other2.651
r_mcbond_it1.81
r_mcbond_other1.809
r_angle_refined_deg1.677
r_angle_other_deg0.971
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms2189
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing