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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K/P192S) in complex with NADP
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, Lithium acetate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.125 α = 90 b = 99.133 β = 90 c = 152.878 γ = 90
Symmetry Space Group P 21 21 21
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 50 99.7 0.987 0.082 0.994 7.1 3.8 86317
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 99.3 0.506 3.3
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 38.97 86317 4572 99.64 0.1734 0.17059 0.1805 0.22729 0.2327 RANDOM 26.521
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] -2.17 1.89 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.01 r_dihedral_angle_2_deg 11.126 r_dihedral_angle_1_deg 7.749 r_long_range_B_refined 7.2 r_long_range_B_other 7.2 r_scangle_other 5.673 r_scbond_it 3.712 r_scbond_other 3.712 r_mcangle_it 3.65 r_mcangle_other 3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.01 r_dihedral_angle_2_deg 11.126 r_dihedral_angle_1_deg 7.749 r_long_range_B_refined 7.2 r_long_range_B_other 7.2 r_scangle_other 5.673 r_scbond_it 3.712 r_scbond_other 3.712 r_mcangle_it 3.65 r_mcangle_other 3.65 r_mcbond_it 2.554 r_mcbond_other 2.554 r_angle_refined_deg 1.62 r_angle_other_deg 0.536 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 10164 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms 210
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement HKL-2000 data scaling MOLREP phasing