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CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 100 MM IMIDAZOLE PH 6.5, 20% PEG
3350, 100 MM MAGNESIUM CHLORIDE, 2M NACL, 1MM NADH; SOAK
OVERNIGHT IN CRYSTALLIZATION SOLUTION PLUS 5 MM 3-
PHOSPHOGLYCERATE; 20% EG CRYO, VAPOR DIFFUSION, TEMPERATURE
289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.11 α = 89.64 b = 59.62 β = 89.83 c = 63.48 γ = 79.36
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 2014-06-12 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) 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 1.77 28.36 96.5 0.05 15.19 2.65 58407 -3 28.9
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 1.77 1.82 95.1 0.5 2.8
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 2G76 1.77 28.36 58386 2904 96.4 0.193 0.192 0.1938 0.223 0.2227 36.59
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 4044 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 110
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling