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Crystal structure of Neanderthal Adenylosuccinate Lyase (ADSL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 19-21% PEG6000, 0.1 M Tris pH 8
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.39 α = 90 b = 104.88 β = 90 c = 215.4 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2015-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.7 48 99.5 0.116 0.998 9.8 4.6 211102 29
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 1.7 1.8 99.8 1.3 0.42 1.2 4.7
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 2J91 1.7 19.96 200295 10542 99.3 0.17343 0.17126 0.1822 0.21493 0.2225 RANDOM 31.021
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 -0.93 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.065 r_dihedral_angle_4_deg 19.123 r_dihedral_angle_3_deg 13.965 r_long_range_B_refined 7.203 r_long_range_B_other 7.203 r_dihedral_angle_1_deg 6.223 r_scangle_other 5.78 r_scbond_it 3.85 r_scbond_other 3.849 r_angle_other_deg 3.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.065 r_dihedral_angle_4_deg 19.123 r_dihedral_angle_3_deg 13.965 r_long_range_B_refined 7.203 r_long_range_B_other 7.203 r_dihedral_angle_1_deg 6.223 r_scangle_other 5.78 r_scbond_it 3.85 r_scbond_other 3.849 r_angle_other_deg 3.558 r_mcangle_it 3.436 r_mcangle_other 3.436 r_mcbond_it 2.532 r_mcbond_other 2.531 r_angle_refined_deg 1.496 r_chiral_restr 0.099 r_gen_planes_other 0.018 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 Atoms Number Protein Atoms 14636 Nucleic Acid Atoms Solvent Atoms 1191 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing