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Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2 M MgCl2, 0.1 M Tris pH 7, and 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.69 α = 90 b = 101.69 β = 90 c = 271.68 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 30 99.9 0.98 9.3 5.65 73339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.95 0.61
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5XVI 2.85 29.89 69568 3769 99.955 0.196 0.1919 0.1971 0.2677 0.2592 47.117
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] -5.363 -5.363 10.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.858 r_dihedral_angle_6_deg 14.418 r_lrange_it 13.355 r_lrange_other 13.354 r_dihedral_angle_2_deg 9.258 r_dihedral_angle_1_deg 7.835 r_mcangle_it 6.666 r_mcangle_other 6.666 r_scangle_it 5.396 r_scangle_other 5.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.858 r_dihedral_angle_6_deg 14.418 r_lrange_it 13.355 r_lrange_other 13.354 r_dihedral_angle_2_deg 9.258 r_dihedral_angle_1_deg 7.835 r_mcangle_it 6.666 r_mcangle_other 6.666 r_scangle_it 5.396 r_scangle_other 5.396 r_mcbond_it 4.032 r_mcbond_other 4.032 r_scbond_it 3.145 r_scbond_other 3.145 r_angle_refined_deg 1.654 r_symmetry_xyhbond_nbd_refined 0.713 r_angle_other_deg 0.585 r_symmetry_nbd_refined 0.493 r_nbd_other 0.409 r_xyhbond_nbd_other 0.247 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.215 r_ncsr_local_group_3 0.212 r_ncsr_local_group_14 0.212 r_ncsr_local_group_13 0.211 r_nbd_refined 0.209 r_ncsr_local_group_11 0.209 r_ncsr_local_group_10 0.208 r_ncsr_local_group_4 0.207 r_ncsr_local_group_15 0.207 r_ncsr_local_group_7 0.206 r_ncsr_local_group_8 0.205 r_ncsr_local_group_2 0.2 r_ncsr_local_group_12 0.2 r_ncsr_local_group_9 0.199 r_ncsr_local_group_6 0.198 r_ncsr_local_group_5 0.197 r_ncsr_local_group_1 0.191 r_nbtor_refined 0.177 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbtor_other 0.084 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20802 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BALBES phasing