8S0V | pdb_00008s0v

Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ELO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.136α = 90
b = 116.697β = 90
c = 142.882γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95373DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.658.3599.70.0820.0330.9991613.116092519.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.63951.2120.6350.6281.68.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.658.35160837814699.6970.1850.18430.1940.20850.217522.791
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]
0.0680.804-0.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.11
r_dihedral_angle_3_deg14.28
r_dihedral_angle_2_deg9.846
r_dihedral_angle_1_deg6.908
r_lrange_it6.141
r_lrange_other6.115
r_scangle_it5.14
r_scangle_other5.139
r_scbond_it3.467
r_scbond_other3.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.11
r_dihedral_angle_3_deg14.28
r_dihedral_angle_2_deg9.846
r_dihedral_angle_1_deg6.908
r_lrange_it6.141
r_lrange_other6.115
r_scangle_it5.14
r_scangle_other5.139
r_scbond_it3.467
r_scbond_other3.464
r_mcangle_it2.91
r_mcangle_other2.91
r_dihedral_angle_other_2_deg2.47
r_mcbond_it2.133
r_mcbond_other2.133
r_angle_refined_deg1.666
r_angle_other_deg0.573
r_symmetry_nbd_refined0.256
r_nbd_refined0.217
r_symmetry_xyhbond_nbd_other0.189
r_symmetry_nbd_other0.185
r_nbtor_refined0.183
r_symmetry_xyhbond_nbd_refined0.178
r_nbd_other0.148
r_xyhbond_nbd_refined0.133
r_chiral_restr0.096
r_ncsr_local_group_10.089
r_symmetry_nbtor_other0.08
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8051
Nucleic Acid Atoms
Solvent Atoms754
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing