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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 (L36S/T37K/F100V/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, Ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.971 α = 90 b = 119.991 β = 90 c = 144.687 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) 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 90.8 0.978 7.2 2.4 88673
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 81.4 0.268 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 36.72 88673 4642 96.88 0.17013 0.16775 0.1768 0.21457 0.2177 RANDOM 24.307
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] -0.78 -0.32 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.176 r_dihedral_angle_2_deg 9.575 r_dihedral_angle_1_deg 7.666 r_long_range_B_refined 5.833 r_long_range_B_other 5.832 r_scangle_other 4.447 r_scbond_it 2.822 r_scbond_other 2.822 r_mcangle_it 2.75 r_mcangle_other 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.176 r_dihedral_angle_2_deg 9.575 r_dihedral_angle_1_deg 7.666 r_long_range_B_refined 5.833 r_long_range_B_other 5.832 r_scangle_other 4.447 r_scbond_it 2.822 r_scbond_other 2.822 r_mcangle_it 2.75 r_mcangle_other 2.75 r_mcbond_it 1.918 r_mcbond_other 1.918 r_angle_refined_deg 1.384 r_angle_other_deg 0.471 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 10165 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 220
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement HKL-2000 data scaling MOLREP phasing