6HCW

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529125% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.6353.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.514α = 90
b = 142.65β = 90
c = 72.939γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.969DiamondI24

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
11.467397.60.076105.6205432
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.580.50.6590.561.42.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5ELN1.4672.941941821023797.140.18860.18720.2149RANDOM15.952
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]
0.7-0.19-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.968
r_dihedral_angle_4_deg14.52
r_dihedral_angle_3_deg12.684
r_dihedral_angle_1_deg6.716
r_angle_refined_deg1.929
r_angle_other_deg1.065
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.968
r_dihedral_angle_4_deg14.52
r_dihedral_angle_3_deg12.684
r_dihedral_angle_1_deg6.716
r_angle_refined_deg1.929
r_angle_other_deg1.065
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8023
Nucleic Acid Atoms
Solvent Atoms907
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data scaling
MOLREPphasing