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YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.75 292 Crystal produced from streak seeding. Mother liquor: 26% w/v PEG 3350, 400 mM (NH4)2SO4, and 70 mM BisTris-HCl pH 6.75. Protein buffer: 50 mM NaCl, 50 mM Tris-HCl pH 7.4, 4% 1-,4-dioxane, and 0.1 mM TCEP.
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.36 α = 90 b = 74.48 β = 92.29 c = 141.06 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 MAR CCD 165 mm 2009-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9537 SLS X06SA
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 2.34 31.72 87 0.1559 11.68 4 60390 12.18
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 2.34 2.424 36 0.276 4.59 1.3
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 1YAC 2.34020690848 31.72 1.33592006581 60346 3058 86.8025488701 0.173799820715 0.172182821447 0.1749 0.203845887682 0.2056 Random selection 14.9697430435
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 11.1788438853 f_angle_d 0.670963407373 f_chiral_restr 0.0278780703328 f_plane_restr 0.00266053029077 f_bond_d 0.0023316997053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12488 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 157
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling PHASER phasing