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Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Malonate 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 7 295 2.4 M Na malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 4.05 69.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.15 α = 90 b = 153.74 β = 90 c = 259.88 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++ 2016-07-09 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) 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 1.74 39.39 99.9 0.1 0.11 0.99 16.72 7.2 244015
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 1.74 1.84 99.1 0.83 0.9 0.76 2.39 6.53
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 5XVX 1.74 39.38 231826 12202 99.84 0.14043 0.13924 0.1523 0.16299 0.1745 RANDOM 20.459
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] -1.41 0.36 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.773 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_1_deg 5.942 r_long_range_B_refined 5.926 r_long_range_B_other 5.765 r_scangle_other 4.604 r_scbond_it 3.287 r_scbond_other 3.287 r_mcangle_it 2.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.773 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_1_deg 5.942 r_long_range_B_refined 5.926 r_long_range_B_other 5.765 r_scangle_other 4.604 r_scbond_it 3.287 r_scbond_other 3.287 r_mcangle_it 2.329 r_mcangle_other 2.329 r_angle_refined_deg 2.281 r_mcbond_it 1.882 r_mcbond_other 1.882 r_angle_other_deg 1.154 r_chiral_restr 0.147 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 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 10401 Nucleic Acid Atoms Solvent Atoms 1742 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing