6GQ3

Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-L-norleucine (DON) at 1.85 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CT9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52900.2 M NaCl, 0.1 M sodium HEPES buffer, pH 7.5, and 12% w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 83.52β = 90.65
c = 110.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.8533.6599.80.0870.0670.9969.73.4100002
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)
11.851.8899.90.7940.6240.5121.33.4

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 REPLACEMENTTHROUGHOUT1CT91.8533.6595104487599.80.179910.177640.22462RANDOM33.556
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]
1.45-0.44-0.19-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.001
r_scbond_it29.569
r_scbond_other29.569
r_long_range_B_refined26.186
r_long_range_B_other26.184
r_scangle_other26.126
r_mcbond_other24.517
r_mcbond_it24.514
r_mcangle_it21.259
r_mcangle_other21.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.001
r_scbond_it29.569
r_scbond_other29.569
r_long_range_B_refined26.186
r_long_range_B_other26.184
r_scangle_other26.126
r_mcbond_other24.517
r_mcbond_it24.514
r_mcangle_it21.259
r_mcangle_other21.257
r_dihedral_angle_4_deg14.578
r_dihedral_angle_3_deg12.664
r_dihedral_angle_1_deg6.271
r_angle_other_deg1.479
r_angle_refined_deg1.39
r_chiral_restr0.083
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8244
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing