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aSMase with zinc and phosphocholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 phosphocholine soaked in well solution containing 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 5.0-5.5, 12% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.62 66.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.601 α = 90 b = 131.601 β = 90 c = 188.573 γ = 120
Symmetry Space Group P 64 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 90 CCD RIGAKU SATURN 944+ 2015-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 48.7 99.9 0.2 12.6 17.3 34056 30.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.822 0.9 13.9
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 FREE R-VALUE 5I81 2.5 31.175 1.34 33985 1676 99.92 0.1919 0.1903 0.194 0.2218 0.2227
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 14.043 f_angle_d 0.885 f_chiral_restr 0.048 f_bond_d 0.018 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4161 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 238
Software Software Software Name Purpose PHENIX refinement CrystalClear data collection SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction iMOSFLM data reduction