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Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-ketoglutarate and NADPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M sodium citrate (pH 5.5), 20% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 7.12 82.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.46 α = 90 b = 174.46 β = 90 c = 240.43 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 CCD MARMOSAIC 225 mm CCD 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9763 ESRF BM14
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 1.8 35 99.6 0.092 0.99 17.08 12.2 128967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 97.9 0.41 0.96 5.1 10.9
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 1.8 34 122517 6448 99.65 0.13582 0.13518 0.1484 0.14799 0.1584 RANDOM 29.177
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] 0.21 0.11 0.21 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.899 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 11.931 r_long_range_B_refined 9.045 r_long_range_B_other 7.673 r_dihedral_angle_1_deg 5.98 r_scangle_other 3.932 r_scbond_it 2.661 r_scbond_other 2.654 r_mcangle_other 2.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.899 r_dihedral_angle_4_deg 16.9 r_dihedral_angle_3_deg 11.931 r_long_range_B_refined 9.045 r_long_range_B_other 7.673 r_dihedral_angle_1_deg 5.98 r_scangle_other 3.932 r_scbond_it 2.661 r_scbond_other 2.654 r_mcangle_other 2.235 r_mcangle_it 2.233 r_mcbond_it 1.667 r_mcbond_other 1.661 r_angle_refined_deg 1.654 r_angle_other_deg 0.979 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.006 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 3473 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing