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Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ECS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.86 67.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.12 α = 90 b = 156.12 β = 90 c = 106.07 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 IMAGE PLATE RIGAKU RAXIS IV++ 2021-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.05 40 98.9 0.17 0.99 11.9 10.8 95195 26.24
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 2.05 2.15 92.3 0.58
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 7ECS 2.05 29.77 87330 4670 99.99 0.1774 0.17601 0.2021 0.203 0.23 RANDOM 28.029
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] 1.94 1.94 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.898 r_dihedral_angle_4_deg 17.354 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_1_deg 7.269 r_long_range_B_refined 5.704 r_long_range_B_other 5.686 r_scangle_other 4.425 r_mcangle_it 3.727 r_mcangle_other 3.727 r_scbond_it 3.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.898 r_dihedral_angle_4_deg 17.354 r_dihedral_angle_3_deg 15.804 r_dihedral_angle_1_deg 7.269 r_long_range_B_refined 5.704 r_long_range_B_other 5.686 r_scangle_other 4.425 r_mcangle_it 3.727 r_mcangle_other 3.727 r_scbond_it 3.314 r_scbond_other 3.314 r_mcbond_it 2.957 r_mcbond_other 2.957 r_angle_refined_deg 1.763 r_angle_other_deg 1.434 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 6908 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BALBES phasing