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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NAD and G3P
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, Ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.946 α = 90 b = 119.849 β = 91.27 c = 140.632 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 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) 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 1.99 50 90.7 0.994 10.1 1.8 176119
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 2.03 90.1 0.275 1.8
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 1.99 32.86 176119 9120 94.55 0.16567 0.16386 0.175 0.20065 0.2077 RANDOM 25.848
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] -0.84 -0.05 -0.3 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.208 r_dihedral_angle_2_deg 11.548 r_dihedral_angle_1_deg 7.55 r_long_range_B_refined 6.653 r_long_range_B_other 6.653 r_scangle_other 4.961 r_scbond_it 3.287 r_scbond_other 3.287 r_mcangle_other 3.223 r_mcangle_it 3.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.208 r_dihedral_angle_2_deg 11.548 r_dihedral_angle_1_deg 7.55 r_long_range_B_refined 6.653 r_long_range_B_other 6.653 r_scangle_other 4.961 r_scbond_it 3.287 r_scbond_other 3.287 r_mcangle_other 3.223 r_mcangle_it 3.222 r_mcbond_it 2.343 r_mcbond_other 2.342 r_angle_refined_deg 1.519 r_angle_other_deg 0.511 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 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 20273 Nucleic Acid Atoms Solvent Atoms 1393 Heterogen Atoms 553
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement HKL-2000 data scaling MOLREP phasing