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Crystal structure of NADP-specific glutamate dehydrogenase Gdh1 from Schizosaccharomyces pombe in complex with alpha-iminoglutarate and NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GUD 5GUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES-NaOH, pH 7.5, 1.6M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.965 α = 90 b = 96.965 β = 90 c = 188.258 γ = 120
Symmetry Space Group P 63 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 95 PIXEL DECTRIS PILATUS3 S 2M 2019-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 1.45 46.99 99.9 0.076 0.078 0.018 0.999 21.5 19 92864
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 1.45 1.47 99.1 0.931 0.962 0.241 0.884 15.6
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 5GUD 1.45 46.99 88100 4666 99.84 0.18095 0.17942 0.1819 0.20967 0.2133 RANDOM 21.646
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] 2.46 1.23 2.46 -7.99
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.03 r_long_range_B_other 12.084 r_dihedral_angle_3_deg 12.061 r_scangle_other 9.829 r_dihedral_angle_2_deg 7.963 r_scbond_it 7.419 r_scbond_other 7.39 r_mcangle_it 7.279 r_mcangle_other 7.279 r_dihedral_angle_1_deg 6.086
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.03 r_long_range_B_other 12.084 r_dihedral_angle_3_deg 12.061 r_scangle_other 9.829 r_dihedral_angle_2_deg 7.963 r_scbond_it 7.419 r_scbond_other 7.39 r_mcangle_it 7.279 r_mcangle_other 7.279 r_dihedral_angle_1_deg 6.086 r_mcbond_it 5.98 r_mcbond_other 5.978 r_rigid_bond_restr 4.656 r_angle_refined_deg 1.782 r_angle_other_deg 0.648 r_chiral_restr 0.102 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3414 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing