☰ Navigation Tabs
Crystal structure of the mature 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 K/Na-tartrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.51 50.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.934 α = 90 b = 130.661 β = 90 c = 171.864 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 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 2.25 40 97.1 0.061 11.7 6.7 87235 87235 -3 23.3
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 2.25 2.32 90.6 0.297 1.9 5.6
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 1PJ5 2.26 40 85428 1743 96.67 0.24128 0.24075 0.2438 0.26739 0.2673 RANDOM 25.719
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] 0.52 1.14 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 15.253 r_dihedral_angle_1_deg 5.799 r_long_range_B_refined 3.147 r_long_range_B_other 3.133 r_mcangle_it 1.771 r_mcangle_other 1.771 r_scangle_other 1.734 r_angle_refined_deg 1.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.11 r_dihedral_angle_3_deg 15.306 r_dihedral_angle_4_deg 15.253 r_dihedral_angle_1_deg 5.799 r_long_range_B_refined 3.147 r_long_range_B_other 3.133 r_mcangle_it 1.771 r_mcangle_other 1.771 r_scangle_other 1.734 r_angle_refined_deg 1.168 r_mcbond_it 1.048 r_mcbond_other 1.047 r_scbond_it 0.998 r_scbond_other 0.998 r_angle_other_deg 0.882 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 12952 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement