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Directed evolution and rational design of a de novo designed esterase toward improved catalysis. Northeast Structural Genomics Consortium (NESG) Target OR184
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U10 PDB ENTRY 3U10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Potassium Bromide 0.1M,mMES 0.1M, PEG4000 40% (w/v), microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.02 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.201 α = 90 b = 90.122 β = 90 c = 137.349 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 CCD ADSC QUANTUM 4 2012-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97942 NSLS X4A
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 2.23 50 100 0.124 18.8 5.3 38878 -3 20.5
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3U10 2.29 29.82 1.44 67776 3364 99.43 0.1686 0.1652 0.1658 0.2323 0.2319 19.997
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 14.309 f_angle_d 1.08 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6532 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing