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Perdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE
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 293.15 0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT,18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.323 α = 90 b = 52.678 β = 117.86 c = 58.665 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 PIXEL DECTRIS PILATUS3 6M 2016-11-01 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 PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.89 PETRA III, EMBL c/o DESY P14 (MX2) 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 1.1 45.01 96 0.043 0.999 14.77 3.2 104600 2 1.8 40 78 0.194 0.955 3.8 5.2 19145
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 1.1 1.16 0.96 0.663 2.1 2 1.8 1.9 0.514 0.666 2.5
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 1.1 45.01 1.35 104575 5194 96.17 0.1444 0.1437 0.1445 0.1576 0.1588 23.4706 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.8 30.5502 19144 965 77.37 0.222 0.2201 0.2593
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 19.626 f_angle_d 1.393 f_chiral_restr 0.099 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1871 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction LAUEGEN data reduction XSCALE data scaling SCALA data scaling PHASER phasing