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Glutamate dehydrogenase-AKG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM MES buffer (pH 6.5), 10% (w/v) PEG5,000 MME, 12% (v/v) 1-propanol, and 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.267 α = 90 b = 156.419 β = 110.3 c = 99.33 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.73 47.21 100 0.143 0.156 0.06 0.996 7.8 6.7 141497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 99.4 0.933 1.034 0.437 0.789 5.4
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 1.73 47.21 134338 7121 99.94 0.19826 0.19655 0.2075 0.23065 0.2388 RANDOM 20.957
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] -1.35 0.59 -1.58 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.781 r_dihedral_angle_2_deg 9.698 r_dihedral_angle_1_deg 6.374 r_long_range_B_refined 4.77 r_long_range_B_other 4.734 r_scangle_other 3.327 r_mcangle_it 2.404 r_mcangle_other 2.404 r_scbond_it 2.203 r_scbond_other 2.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.781 r_dihedral_angle_2_deg 9.698 r_dihedral_angle_1_deg 6.374 r_long_range_B_refined 4.77 r_long_range_B_other 4.734 r_scangle_other 3.327 r_mcangle_it 2.404 r_mcangle_other 2.404 r_scbond_it 2.203 r_scbond_other 2.203 r_mcbond_it 1.657 r_mcbond_other 1.657 r_angle_refined_deg 1.595 r_angle_other_deg 1.042 r_chiral_restr 0.084 r_bond_other_d 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9480 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing