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Crystal Structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1 covalently bound with FP-alkyne, Northeast Structural Genomics Consortium (NESG) Target OR273
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V45 PDB ENTRY 3V45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 4.2 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:RbCl 0.1M, Sodium Citrate 0.1M, PEG1000 40%, , microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.846 α = 90 b = 66.977 β = 100.27 c = 37.911 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 100 CCD ADSC QUANTUM 4 mirrors 2012-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 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 1.36 50 90.3 0.09 43.5 6.9 32937 -3 10.98
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3V45 1.36 33.488 1.34 32931 1670 90.08 0.145 0.145 0.147 0.161 0.1632 random 16.414
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 15.58 f_angle_d 1.082 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1194 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing