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Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 295 0.2 M Sodium tartrate dibasic, 20% PEG3350 pH 7.3
Crystal Properties Matthews coefficient Solvent content 4.03 69.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.86 α = 90 b = 153.09 β = 90 c = 259.27 γ = 90
Symmetry Space Group I 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2018-08-24 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) 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 2.9 39.29 99.8 0.42 0.46 0.96 4.73 6.7 53084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 1.52 1.65 0.65 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XVX 2.9 39.29 50428 2655 99.85 0.22491 0.22254 0.26853 0.2257 RANDOM 41.35
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] -6.11 -0.96 7.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.93 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_4_deg 15.659 r_dihedral_angle_1_deg 6.26 r_long_range_B_refined 4.821 r_long_range_B_other 4.821 r_mcangle_it 3.213 r_mcangle_other 3.213 r_scangle_other 2.982 r_mcbond_it 1.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.93 r_dihedral_angle_3_deg 16.262 r_dihedral_angle_4_deg 15.659 r_dihedral_angle_1_deg 6.26 r_long_range_B_refined 4.821 r_long_range_B_other 4.821 r_mcangle_it 3.213 r_mcangle_other 3.213 r_scangle_other 2.982 r_mcbond_it 1.986 r_mcbond_other 1.986 r_scbond_it 1.767 r_scbond_other 1.765 r_angle_refined_deg 1.587 r_angle_other_deg 0.989 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 10376 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 246
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing