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Three-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:0.1M Ammonium Sulfate, 0.1M MES, 40% PEG 8000, microbatch under oil
Crystal Properties Matthews coefficient Solvent content 2.13 42.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.644 α = 90 b = 62.052 β = 90 c = 107.067 γ = 90
Symmetry Space Group I 2 2 2
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 MAR CCD 165 mm mirrors 2012-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.1 50 95.8 0.081 37 12.7 10802 -3 24.2
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 BALBES THROUGHOUT 2BFR 2.113 41.427 1.34 10795 520 98.31 0.175 0.172 0.1711 0.239 0.2325 random 32.397
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] -4.39 -3.212 7.603
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.144 f_angle_d 1.003 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1456 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction msr165 data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing