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Crystal structure of human aminoadipate semialdehyde synthase, saccharopine dehydrogenase domain with proline bound.
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 -- 0.2M sodium malonate -- 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.22 61.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.374 α = 90 b = 102.414 β = 90 c = 142.074 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 PILATUS3 S 6M 2017-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 2.71 83.03 100 0.113 0.998 12.6 6.6 37204 48.72
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 2.71 2.76 99.9 0.615 1.4 6.9
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 2.48 83.08 42985 2169 92.83 0.32304 0.32181 0.3219 0.34754 0.3484 RANDOM 61.296
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] 0.86 1.96 -2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.442 r_dihedral_angle_3_deg 10.895 r_dihedral_angle_4_deg 7.887 r_dihedral_angle_1_deg 4.082 r_long_range_B_refined 2.157 r_long_range_B_other 2.157 r_mcangle_it 1.318 r_mcangle_other 1.318 r_angle_refined_deg 0.923 r_angle_other_deg 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.442 r_dihedral_angle_3_deg 10.895 r_dihedral_angle_4_deg 7.887 r_dihedral_angle_1_deg 4.082 r_long_range_B_refined 2.157 r_long_range_B_other 2.157 r_mcangle_it 1.318 r_mcangle_other 1.318 r_angle_refined_deg 0.923 r_angle_other_deg 0.81 r_scangle_other 0.752 r_mcbond_it 0.708 r_mcbond_other 0.708 r_scbond_it 0.369 r_scbond_other 0.369 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 6485 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing