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Crystal structure of the precursor form of rat DMGDH complexed with tetrahydrofolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M NaSCN, 20% PEG 3350, 0.1 M Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.182 α = 90 b = 107.215 β = 92.16 c = 114.466 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 MARMOSAIC 225 mm CCD 2013-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 48.19 96.7 0.037 22.2 5.7 167803 167803 -3 21.6
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 1.85 1.9 90.2 0.392 1.5 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PJ5 1.85 48.19 163455 3356 96.39 0.20697 0.20648 0.23053 0.2161 RANDOM 35.572
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] 1.43 2.73 1.23 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_3_deg 13.317 r_dihedral_angle_1_deg 5.987 r_long_range_B_refined 4.044 r_long_range_B_other 3.976 r_scangle_other 1.974 r_mcangle_it 1.366 r_mcangle_other 1.366 r_angle_refined_deg 1.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_4_deg 15.562 r_dihedral_angle_3_deg 13.317 r_dihedral_angle_1_deg 5.987 r_long_range_B_refined 4.044 r_long_range_B_other 3.976 r_scangle_other 1.974 r_mcangle_it 1.366 r_mcangle_other 1.366 r_angle_refined_deg 1.288 r_scbond_it 1.248 r_scbond_other 1.23 r_mcbond_it 0.895 r_mcbond_other 0.875 r_angle_other_deg 0.856 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 13063 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement