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Perdeuterated E65Q-TIM complexed with 2-PHOSPHOGLYCOLIC ACID
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293.15 0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT, 18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.341 α = 90 b = 52.365 β = 118.03 c = 58.463 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 315 2018-04-23 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE CUSTOM-MADE 2018-03-28 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.98 ESRF BM30A 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.7-3.5 ILL LADI III
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.15 45.674 99.4 0.049 0.999 23.49 4.9 95584 2 1.7 40 88.6 0.097 0.997 13.3 6.6 25565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.18 0.617 0.767 2.47 2 1.7 1.79 0.367 0.924 5.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.15 25.3325 1.35 95574 1998 99.48 0.1404 0.1402 0.1398 0.1527 0.1531 26 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.7 30.3961 25544 533 88.01 0.1828 0.1839 0.2209 26.2
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 18.049 f_angle_d 1.223 f_chiral_restr 0.091 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement LAUEGEN data reduction XDS data reduction XSCALE data scaling SCALA data scaling PHASER phasing