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Crystal structure of glutamate dehydrogenase(GDH) from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 PEG 3350, Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.219 α = 90 b = 93.032 β = 108.16 c = 187.875 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 270 2014-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.29 178.51 98.6 21.14 5.6 249267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34
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 1BGV 2.29 34.366 233608 12145 97.7 0.1674 0.1646 0.1729 0.2224 0.2253 RANDOM 25.987
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] -0.46 -0.16 -0.61 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 15.878 r_dihedral_angle_1_deg 6.692 r_mcangle_it 3.275 r_mcbond_it 2.074 r_mcbond_other 2.073 r_angle_refined_deg 1.789 r_angle_other_deg 1.076 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.413 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_3_deg 15.878 r_dihedral_angle_1_deg 6.692 r_mcangle_it 3.275 r_mcbond_it 2.074 r_mcbond_other 2.073 r_angle_refined_deg 1.789 r_angle_other_deg 1.076 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40276 Nucleic Acid Atoms Solvent Atoms 1632 Heterogen Atoms 522
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing