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Crystal structure of the mature form of rat DMGDH
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 7.4 293 0.2 M K/Na-tartrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.211 α = 90 b = 131.442 β = 90 c = 171.924 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 2.3 40 91.1 0.076 13.7 5.6 75192 75192 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37 85.5 0.298 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 2.32 40 73606 1517 89.68 0.25388 0.25304 0.2555 0.29479 0.2903 RANDOM 30.831
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] 0.33 1.36 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.447 r_dihedral_angle_3_deg 17.158 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_1_deg 6.461 r_long_range_B_refined 4.648 r_long_range_B_other 4.646 r_mcangle_it 3.003 r_scangle_other 3.003 r_mcangle_other 3.002 r_mcbond_it 1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.447 r_dihedral_angle_3_deg 17.158 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_1_deg 6.461 r_long_range_B_refined 4.648 r_long_range_B_other 4.646 r_mcangle_it 3.003 r_scangle_other 3.003 r_mcangle_other 3.002 r_mcbond_it 1.924 r_mcbond_other 1.924 r_scbond_it 1.87 r_scbond_other 1.87 r_angle_refined_deg 1.444 r_angle_other_deg 1.002 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 104 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement