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A fungal glyceraldehyde-3-phosphate dehydrogenase with self-resistance to inhibitor heptelidic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.15 0.1 M sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.45 49.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.667 α = 90 b = 96.562 β = 96.949 c = 96.699 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 PILATUS3 S 6M 2018-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97930 SSRF BL18U1
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 2.059 50 98.6 0.126 0.837 2.429 5.8 85148 -3 25.100858583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.1 0.583 0.837 2.429
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4O59 2.05990923752 39.2901171738 1.36645748307 78233 3859 90.4793847221 0.152561571772 0.150416608 0.1519 0.193344350312 0.1946 26.7337282741
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 15.3791994224 f_angle_d 0.999394911836 f_chiral_restr 0.0557773820079 f_bond_d 0.00616120224869 f_plane_restr 0.00555418861373
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10132 Nucleic Acid Atoms Solvent Atoms 647 Heterogen Atoms 344
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing