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Crystal structure of a de novo retro-aldolase catalyzing asymmetric Michael additions, with a covalently bound product analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 Crystals were obtained at 4 degrees C using the sitting drop vapor diffusion method by mixing 100 nL of protein solution (13.5 mg/mL) in buffer with 100 nL of reservoir solution containing 2 M ammonium sulfate and 0.1 M BIS-TRIS buffer pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.557 α = 90 b = 68.804 β = 90 c = 69.341 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 PILATUS 2M-F 2013-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 46.45 99.8 0.031 0.013 24.2 6.2 94052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 96.3 0.811 0.383 2.1 5.4 4466
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 FREE R-VALUE 4A29 1.2 46.3 93775 4653 99.8 0.139 0.1363 0.177 0.169 random selection 22.5577
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 1836 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 37
Software Software Software Name Purpose Aimless data scaling SHELXL refinement PDB_EXTRACT data extraction PHASER phasing