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Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 286 0.1M tris pH 7.5 -- 0.33M sodium malonate -- 19.5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.462 α = 90 b = 91.462 β = 90 c = 150.353 γ = 90
Symmetry Space Group P 43 21 2
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 S 6M 2017-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928190 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 49.03 100 0.112 0.973 12.2 13.2 51064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.204 1 12.6
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 5l76 1.9 49.03 48427 2554 99.98 0.31128 0.31065 0.3177 0.32284 0.3282 RANDOM 80.955
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] 2.63 2.63 -5.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.887 r_dihedral_angle_4_deg 12.161 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 4.605 r_long_range_B_refined 4.532 r_long_range_B_other 4.476 r_mcangle_it 2.806 r_mcangle_other 2.806 r_scangle_other 2.05 r_mcbond_it 1.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.887 r_dihedral_angle_4_deg 12.161 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 4.605 r_long_range_B_refined 4.532 r_long_range_B_other 4.476 r_mcangle_it 2.806 r_mcangle_other 2.806 r_scangle_other 2.05 r_mcbond_it 1.565 r_mcbond_other 1.565 r_scbond_it 1.078 r_scbond_other 1.078 r_angle_refined_deg 1.008 r_angle_other_deg 0.833 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3317 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing