5FOM | pdb_00005fom

Crystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with the adduct AMP-AN6426


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
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.065α = 90
b = 65.065β = 90
c = 167.301γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 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
12.160.641000.042910.4219742
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)
12.12.2990.475.610.6

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 2WFG2.160.6420768112299.80.201350.199410.210.238660.24RANDOM55.3
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]
3.593.59-7.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.741
r_dihedral_angle_4_deg15.893
r_dihedral_angle_3_deg15.278
r_dihedral_angle_1_deg6.383
r_mcangle_it4.364
r_scbond_it3.723
r_mcbond_it3.042
r_mcbond_other3.035
r_angle_refined_deg1.667
r_angle_other_deg0.927
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.741
r_dihedral_angle_4_deg15.893
r_dihedral_angle_3_deg15.278
r_dihedral_angle_1_deg6.383
r_mcangle_it4.364
r_scbond_it3.723
r_mcbond_it3.042
r_mcbond_other3.035
r_angle_refined_deg1.667
r_angle_other_deg0.927
r_chiral_restr0.128
r_bond_refined_d0.01
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms2189
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing