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Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma genitalium with bound NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 MygeA.00914.a.B2.PW38693 at 18 mg/ml incubated with 3 mM glycerol-3-phosphate and NAD, then mixed 1:1 with MorpheusII(f11): 10%(w/v) PEG 8K, 20%(w/v) 1,5-pentanediol, 0.1 M GlyGly/AMPD pH 8.5, 0.02 M of each xylitol, D-(--fructose, D-sorbitol, myo-inositol, L-rhamnose monohydrate. Tray: 312789f11. Puck: pvq3-6.
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.6 α = 90 b = 94.17 β = 90 c = 172.8 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 RAYONIX MX-300 Beryllium Lenses 2020-03-19 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 Merge I (Observed) Rrim 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 2.2 45.43 99.9 0.081 0.087 0.998 14.58 7.134 76513 47.822
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 100 0.576 0.62 0.91 3.62 7.223
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VMT 2.2 45.43 73816 4556 96.44 0.1608 0.1585 0.161 0.1966 0.1986 51.8934
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 16.126 f_angle_d 0.837 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9975 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 244
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing