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Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)in complex with its products AICAR and fumarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 20 % ethylene glycol, 10 % PEG8000, 0.1 M imidazole/MES pH 6.5, 0.12 M alcohols
(Morpheus screen Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.25 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 356.53 α = 90 b = 74.21 β = 108.99 c = 160.31 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2016-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 49 99 0.22 0.99 6.8 4.5 153910 42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 99.9 1.39 0.45 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NX8 2.4 47.85 146181 7694 98.91 0.22198 0.22027 0.2244 0.25428 0.2553 RANDOM 52.07
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] 0.37 1.68 -2.39 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.511 r_dihedral_angle_4_deg 19.131 r_dihedral_angle_3_deg 15.47 r_long_range_B_refined 7.751 r_long_range_B_other 7.751 r_scangle_other 5.935 r_dihedral_angle_1_deg 5.814 r_mcangle_it 4.89 r_mcangle_other 4.89 r_scbond_it 3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.511 r_dihedral_angle_4_deg 19.131 r_dihedral_angle_3_deg 15.47 r_long_range_B_refined 7.751 r_long_range_B_other 7.751 r_scangle_other 5.935 r_dihedral_angle_1_deg 5.814 r_mcangle_it 4.89 r_mcangle_other 4.89 r_scbond_it 3.83 r_scbond_other 3.83 r_angle_other_deg 3.613 r_mcbond_it 3.3 r_mcbond_other 3.299 r_angle_refined_deg 1.372 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 28814 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing