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Structure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 75mM NaCH02, and 100mM BTP pH 6.0). Cryoprotected with 20% PEG 3350, 75mM NaCH02, 25mM laminaritriose, 100mM BTP pH 6.0 and 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.775 α = 90 b = 100.195 β = 103.49 c = 53.862 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD mirrors and beryllium lenses 2013-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.4 50 100 0.065 9.5 3.9 100816 14.55
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 1.4 1.42 99.9 0.481 3.3
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 4PEW 1.5 24.23 1.36 81427 4085 99.4 0.116 0.115 0.1167 0.144 0.1437 Random selection 18
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 12.306 f_angle_d 1.13 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4167 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PHASER phasing DENZO data reduction SCALEPACK data scaling