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Crystal structure of human dimethylglycine-dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293.15 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each amino acid and 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.377 α = 90 b = 119.868 β = 92.58 c = 86.466 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 PIXEL DECTRIS PILATUS 6M 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.09 58.651 97.7 0.2058 0.958 4.81 2.8 30495 47.09
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 3.09 3.2 93.81 0.6573 1.53 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4PAA 3.09 58.651 1.37 30482 1524 97.66 0.1835 0.179 0.1864 0.2693 0.2718 random 38.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.056 f_angle_d 1.373 f_chiral_restr 0.054 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12782 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing