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crystal structure of N-ethylmaleimide reductase with mutation Y187F (nemA Y187F) from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P7Y 3P7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 288.15 0.2 M Potassium bromide,
0.2 M Potassium thiocyanate,
0.1 M Tris pH 7.8,
3 % w/v PGA (Na+ form, LM)
2 % w/v PEG 3350
5 mM Tb-XO4
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.062 α = 90 b = 96.062 β = 90 c = 100.35 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS 6M 2022-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (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 2.1 24.271 99.9 0.442 0.467 0.148 6.4 9.9 45797 17.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 1.222 1.222 1.285 0.396 0.6 10.5
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 THROUGHOUT 3P7Y 2.3 24.27 1.96 45797 2001 99.47 0.1955 0.1932 0.1932 0.2446 0.2447 26.4277
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 8307 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 183
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing