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Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Isophthalate and NADPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 0.1 M MES (pH 6.0) 30% (v/v) PEG 200, 5 % (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 7.06 82.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.48 α = 90 b = 173.48 β = 90 c = 241.14 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 1.9 70 99.9 0.054 0.99 24.3 7.4 109208
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 1.9 2 98.8 0.42 0.61 4.5 6.9
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 1.9 40 103738 5460 99.9 0.16867 0.16805 0.177 0.18038 0.1896 RANDOM 31.006
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] 0.17 0.08 0.17 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.785 r_dihedral_angle_4_deg 18.212 r_dihedral_angle_3_deg 11.756 r_long_range_B_refined 5.939 r_dihedral_angle_1_deg 5.802 r_long_range_B_other 5.66 r_scangle_other 3.835 r_scbond_it 2.422 r_scbond_other 2.406 r_mcangle_other 2.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.785 r_dihedral_angle_4_deg 18.212 r_dihedral_angle_3_deg 11.756 r_long_range_B_refined 5.939 r_dihedral_angle_1_deg 5.802 r_long_range_B_other 5.66 r_scangle_other 3.835 r_scbond_it 2.422 r_scbond_other 2.406 r_mcangle_other 2.401 r_mcangle_it 2.4 r_mcbond_it 1.663 r_mcbond_other 1.661 r_angle_refined_deg 1.444 r_angle_other_deg 0.95 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 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 307 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing