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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K) in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, Cesium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.71 α = 90 b = 117.891 β = 116.92 c = 77.128 γ = 90
Symmetry Space Group C 1 2 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 2021-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.98 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.09 50 92.1 0.991 0.055 0.996 18.3 1.7 39134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.14 87.1 0.24 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 8HRO 2.09 26.71 39134 2077 97.58 0.18023 0.17692 0.1854 0.2455 0.2499 RANDOM 40.838
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] -2.24 -0.9 0.85 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.944 r_dihedral_angle_2_deg 10.659 r_long_range_B_refined 8.845 r_long_range_B_other 8.844 r_dihedral_angle_1_deg 7.884 r_scangle_other 7.496 r_mcangle_other 5.248 r_scbond_it 5.238 r_mcangle_it 5.23 r_scbond_other 5.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.944 r_dihedral_angle_2_deg 10.659 r_long_range_B_refined 8.845 r_long_range_B_other 8.844 r_dihedral_angle_1_deg 7.884 r_scangle_other 7.496 r_mcangle_other 5.248 r_scbond_it 5.238 r_mcangle_it 5.23 r_scbond_other 5.168 r_mcbond_it 4.049 r_mcbond_other 4.037 r_angle_refined_deg 1.591 r_angle_other_deg 0.528 r_chiral_restr 0.074 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5093 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement HKL-2000 data scaling MOLREP phasing