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Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289.15 0.1 M zinc acetate dihydrate, 0.1 M Sodium acetate trihydrate, pH 4.6, 12% w/v polyethylene glycol (PEG) 4000
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.358 α = 90 b = 135.078 β = 90 c = 146.227 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 PIXEL DECTRIS PILATUS3 S 6M 2018-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 1.82 50 99.9 0.111 25.5 10.2 142957 19.228006632
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 1.83 1.86 0.866 0.751
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 1U8F 1.82449538629 43.0321686884 1.33786284913 140724 7010 98.073706512 0.193381921753 0.191578926319 0.1929 0.227886023248 0.2288 24.5209129398
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 7.77193846335 f_angle_d 0.876932321364 f_chiral_restr 0.0610978924302 f_bond_d 0.00631426416622 f_plane_restr 0.00554730802682
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10100 Nucleic Acid Atoms Solvent Atoms 1151 Heterogen Atoms 190
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing