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Crystal structure of SARO_2595 from Novosphingobium aromaticivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8E 3c8e chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Saro protein at 277 mM was incubated with 10 mM reduced glutathione for 50 minutes prior to setting up crystallization experiments. An equal volume of protein solution and reservoir were deposited by a TTP Labtech Mosquito in a SD2 crystallization plate and allowed to equilibrate. The crystals were self-cryoprotected by the reservoir of 4 M ammonium acetate.
Crystal Properties Matthews coefficient Solvent content 3.1 60.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.59 α = 90 b = 70.64 β = 90 c = 168.57 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 EIGER X 16M 2016-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.45 43.97 96.48 0.04367 0.01239 1 36.36 13.2 140421 13.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.502 76.88 0.2047 0.06599 0.986 8.82 10.3
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 FREE R-VALUE 3c8e chain A 1.45 43.975 1.35 140406 1852 96.49 0.1168 0.1165 0.1185 0.1357 0.1375 Thin shells
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 14.535 f_angle_d 1.346 f_chiral_restr 0.079 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4502 Nucleic Acid Atoms Solvent Atoms 972 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing