3HV0

Tryptophanyl-tRNA synthetase from Cryptosporidium parvum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION62930.25 M MgCl2, 0.1 M Bis/Tris pH 6.0, 28% PEG 3350, 10mM ATP, 1mM TCEP, 2mM L-tryptophan, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9637.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.32α = 90
b = 85.22β = 101.91
c = 73.11γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-10-15SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.4243.0795.50.0969.74.425491

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 REPLACEMENTTHROUGHOUTPED ENTRY 3FOC2.424024211127794.950.229230.226930.27286RANDOM21.374
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]
-3.021.38-1.274.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.539
r_dihedral_angle_4_deg23.271
r_dihedral_angle_3_deg18.115
r_dihedral_angle_1_deg6.015
r_scangle_it1.699
r_angle_refined_deg1.198
r_scbond_it1.065
r_angle_other_deg0.899
r_mcangle_it0.598
r_mcbond_it0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.539
r_dihedral_angle_4_deg23.271
r_dihedral_angle_3_deg18.115
r_dihedral_angle_1_deg6.015
r_scangle_it1.699
r_angle_refined_deg1.198
r_scbond_it1.065
r_angle_other_deg0.899
r_mcangle_it0.598
r_mcbond_it0.317
r_mcbond_other0.074
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5586
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms30

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction