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Crystal structure of the diaminopimelate dehydrogenase from Pyrococcus sp. in its holo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.2M Ammonium acetate, 0.1M HEPES pH 7.5, 45% v/v (+/-)-2-Methyl-2,4-pentanedio
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.886 α = 90 b = 165.904 β = 107.72 c = 82.873 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 PIXEL RIGAKU HyPix-6000HE 2025-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 22.08 98.7 0.113 0.124 0.052 0.995 10.8 5.5 162933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 93.9 0.496 0.561 0.256 0.789 4.5
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 1.9 22.08 154622 8220 98.61 0.19963 0.19807 0.2051 0.22893 0.2347 RANDOM 17.562
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] -0.15 -0.41 0.9 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.262 r_dihedral_angle_4_deg 17.317 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 7.328 r_long_range_B_refined 5.037 r_long_range_B_other 4.981 r_scangle_other 3.795 r_mcangle_it 2.758 r_mcangle_other 2.758 r_scbond_it 2.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.262 r_dihedral_angle_4_deg 17.317 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 7.328 r_long_range_B_refined 5.037 r_long_range_B_other 4.981 r_scangle_other 3.795 r_mcangle_it 2.758 r_mcangle_other 2.758 r_scbond_it 2.534 r_scbond_other 2.532 r_mcbond_it 1.903 r_mcbond_other 1.903 r_angle_refined_deg 1.686 r_angle_other_deg 1.379 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 14340 Nucleic Acid Atoms Solvent Atoms 929 Heterogen Atoms 362
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing