5NX9

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527725% PEG1000, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.258

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 107.49β = 90
c = 209.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-11-20MSINGLE 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
12.348.3899.60.2350.9865.73.88641338
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)
12.32.499.81.3890.3561.2

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 REPLACEMENTTHROUGHOUT5NX82.348.3882019431799.470.195060.193420.22654RANDOM40.803
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]
-1.030.970.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.789
r_dihedral_angle_4_deg19.231
r_dihedral_angle_3_deg15.837
r_long_range_B_other8.161
r_long_range_B_refined8.16
r_scangle_other6.478
r_dihedral_angle_1_deg5.92
r_mcangle_it4.196
r_mcangle_other4.196
r_scbond_it4.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.789
r_dihedral_angle_4_deg19.231
r_dihedral_angle_3_deg15.837
r_long_range_B_other8.161
r_long_range_B_refined8.16
r_scangle_other6.478
r_dihedral_angle_1_deg5.92
r_mcangle_it4.196
r_mcangle_other4.196
r_scbond_it4.038
r_scbond_other4.038
r_mcbond_it2.754
r_mcbond_other2.754
r_angle_refined_deg1.232
r_angle_other_deg0.812
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms14840
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms227

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing