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Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Chlamydia trachomatis with bound NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 ChtrB.00839.a.B1.PW38497 (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, and 0.025% Azide) at 17.29 mg/ml was incubated with 4 mM NAD and a small molecule (that is not in the electron density), then was mixed 1:1 with MCSG1(b9): 20% (w/v) PEG-3350, 0.2 M MgCl2, cryo: 20% ethylene glycol. Tray: 307039b9, puck: unc3-9.
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.47 α = 90 b = 135.29 β = 90 c = 137.67 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 2019-02-28 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 2.4 49.688 99.9 0.124 0.135 0.996 11.62 6.24 63802 37.013
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 2.4 2.46 100 0.614 0.671 0.857 3.06 6.309
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 FREE R-VALUE 3PYM 2.4 49.688 59549 3566 93.28 0.1743 0.1721 0.1738 0.2083 0.2097 RANDOM 39.6749
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9876 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 295
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing