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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 8K, HEPES
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.73 α = 90 b = 117.348 β = 116.88 c = 75.815 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) 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 2.59 50 92.8 0.111 14.4 2.6 20397
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 2.59 2.64 84.5 0.274 1.8
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 1DBV 2.59 44.81 20397 992 97.35 0.19025 0.18657 0.1874 0.27154 0.2651 RANDOM 47.959
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] -3.14 -2.5 -0.38 4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.204 r_dihedral_angle_2_deg 11.148 r_long_range_B_refined 10.65 r_long_range_B_other 10.649 r_scangle_other 8.179 r_dihedral_angle_1_deg 7.95 r_mcangle_it 5.839 r_mcangle_other 5.839 r_scbond_it 5.092 r_scbond_other 5.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.204 r_dihedral_angle_2_deg 11.148 r_long_range_B_refined 10.65 r_long_range_B_other 10.649 r_scangle_other 8.179 r_dihedral_angle_1_deg 7.95 r_mcangle_it 5.839 r_mcangle_other 5.839 r_scbond_it 5.092 r_scbond_other 5.091 r_mcbond_it 3.837 r_mcbond_other 3.83 r_angle_refined_deg 1.408 r_angle_other_deg 0.458 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 5083 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 88
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement HKL-2000 data scaling MOLREP phasing