4Q6G

Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829350 mM Tris, pH 8.0, 23% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6666.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.031α = 90
b = 105.031β = 90
c = 70.731γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.24890.90998.70.04841.27.521278210102.62.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2482.3390.60.5382.65.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Q7G2.2590.9092101019912107998.660.187370.185930.21443RANDOM60.752
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]
-1.14-0.57-1.143.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_4_deg12.981
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.818
r_mcangle_it4.81
r_mcbond_it2.784
r_mcbond_other2.778
r_scbond_it2.658
r_angle_refined_deg1.092
r_angle_other_deg0.684
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_4_deg12.981
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.818
r_mcangle_it4.81
r_mcbond_it2.784
r_mcbond_other2.778
r_scbond_it2.658
r_angle_refined_deg1.092
r_angle_other_deg0.684
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.003
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 Atoms2167
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms68

Software

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