5NXA

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)in complex with its products AICAR and fumarate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NX8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720 % ethylene glycol, 10 % PEG8000, 0.1 M imidazole/MES pH 6.5, 0.12 M alcohols (Morpheus screen Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
2.2545.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 356.53α = 90
b = 74.21β = 108.99
c = 160.31γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.967ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.449990.220.996.84.515391042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.599.91.390.454.6

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 REPLACEMENTTHROUGHOUT5NX82.447.85146181769498.910.221980.220270.25428RANDOM52.07
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]
0.371.68-2.390.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg19.131
r_dihedral_angle_3_deg15.47
r_long_range_B_refined7.751
r_long_range_B_other7.751
r_scangle_other5.935
r_dihedral_angle_1_deg5.814
r_mcangle_it4.89
r_mcangle_other4.89
r_scbond_it3.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg19.131
r_dihedral_angle_3_deg15.47
r_long_range_B_refined7.751
r_long_range_B_other7.751
r_scangle_other5.935
r_dihedral_angle_1_deg5.814
r_mcangle_it4.89
r_mcangle_other4.89
r_scbond_it3.83
r_scbond_other3.83
r_angle_other_deg3.613
r_mcbond_it3.3
r_mcbond_other3.299
r_angle_refined_deg1.372
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_other0.011
r_gen_planes_refined0.007
r_bond_other_d
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 Atoms28814
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms248

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing