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Structure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with glucose
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 6.5 298 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, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% PEG 3350, 125mM NaCH02, 75mM Glucose, 100mM BTP pH 6.5 and 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.939 α = 90 b = 100.055 β = 92.31 c = 99.556 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 1.66 50 99.9 0.082 7.2 3.7 123726 15.89
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 1.66 1.69 100 0.546 3.5 6191
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 1.75 24.265 1.35 104871 5253 98.73 0.1423 0.1407 0.1418 0.1721 0.1725 Random selection 17.9898
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 13.292 f_angle_d 1.454 f_chiral_restr 0.088 f_bond_d 0.015 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8339 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 32
Software Software Software Name Purpose PDB_EXTRACT data extraction PHASER phasing PHENIX refinement