5NX8

Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J91 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829319-21% PEG6000, 0.1 M Tris pH 8
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.39α = 90
b = 104.88β = 90
c = 215.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.74899.50.1160.9989.84.621110229
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)
11.71.899.81.30.421.24.7

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 REPLACEMENTTHROUGHOUT2J911.719.962002951054299.30.173430.171260.21493RANDOM31.021
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]
-0.85-0.931.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.065
r_dihedral_angle_4_deg19.123
r_dihedral_angle_3_deg13.965
r_long_range_B_refined7.203
r_long_range_B_other7.203
r_dihedral_angle_1_deg6.223
r_scangle_other5.78
r_scbond_it3.85
r_scbond_other3.849
r_angle_other_deg3.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.065
r_dihedral_angle_4_deg19.123
r_dihedral_angle_3_deg13.965
r_long_range_B_refined7.203
r_long_range_B_other7.203
r_dihedral_angle_1_deg6.223
r_scangle_other5.78
r_scbond_it3.85
r_scbond_other3.849
r_angle_other_deg3.558
r_mcangle_it3.436
r_mcangle_other3.436
r_mcbond_it2.532
r_mcbond_other2.531
r_angle_refined_deg1.496
r_chiral_restr0.099
r_gen_planes_other0.018
r_bond_refined_d0.015
r_gen_planes_refined0.01
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 Atoms14636
Nucleic Acid Atoms
Solvent Atoms1191
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing