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Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 40% v/v PEG 300, 0.1M sodium cacodylate, pH 6.5, 0.2 M calcium acetate hydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.41 α = 90 b = 173.41 β = 90 c = 241.83 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2016-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 35 99 0.11 13.4 7.9 138857
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 1.75 1.85 99.9 0.69 1.9 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 34 131488 6920 98.95 0.15613 0.15545 0.1672 0.16921 0.1808 RANDOM 28.291
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] 0.08 0.04 0.08 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_3_deg 11.976 r_long_range_B_refined 7.923 r_long_range_B_other 7.227 r_dihedral_angle_1_deg 5.822 r_scangle_other 3.928 r_scbond_it 2.628 r_scbond_other 2.628 r_mcangle_other 1.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_4_deg 16.218 r_dihedral_angle_3_deg 11.976 r_long_range_B_refined 7.923 r_long_range_B_other 7.227 r_dihedral_angle_1_deg 5.822 r_scangle_other 3.928 r_scbond_it 2.628 r_scbond_other 2.628 r_mcangle_other 1.957 r_mcangle_it 1.956 r_angle_refined_deg 1.654 r_mcbond_it 1.366 r_mcbond_other 1.362 r_angle_other_deg 0.992 r_chiral_restr 0.201 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 3469 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 370
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing