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Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 20% PEG 3350, 0.1 M NaCl, 0.1 M Tris-Cl, pH 8.5, 0.01 M BaCl2
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.8 α = 103.46 b = 92.82 β = 94.17 c = 111.69 γ = 120.13
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 MARRESEARCH 2013-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.8 40 92 0.06 0.99 11.2 2 69072
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 2.8 2.9 86 0.28 0.84 3.6 1.6
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 3SBO 2.8 35 65578 3451 91.78 0.22987 0.22571 0.2311 0.31011 0.3122 RANDOM 27.449
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] -3.46 -1.4 0.94 -2.29 1.43 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_3_deg 17.868 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_1_deg 6.879 r_long_range_B_refined 3.608 r_long_range_B_other 3.604 r_angle_other_deg 2.083 r_mcangle_it 1.981 r_mcangle_other 1.981 r_scangle_other 1.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.523 r_dihedral_angle_3_deg 17.868 r_dihedral_angle_4_deg 15.882 r_dihedral_angle_1_deg 6.879 r_long_range_B_refined 3.608 r_long_range_B_other 3.604 r_angle_other_deg 2.083 r_mcangle_it 1.981 r_mcangle_other 1.981 r_scangle_other 1.578 r_angle_refined_deg 1.429 r_mcbond_it 1.156 r_mcbond_other 1.156 r_scbond_it 0.891 r_scbond_other 0.891 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 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 20813 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing