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Crystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, with bound D-threonate, domain swapped dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Protein (67.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Threonate); Reservoir (MCSG1(F1); 0.1 M Bis-Tris pH 6.5, 20%(w/v) PEG MME 5000); Cryoprotection (80% Reservoir, 20% ethylene glycol)
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.696 α = 90 b = 47.611 β = 107.12 c = 64.142 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 RAYONIX MX225HE MIRRORS 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.55 61.3 99 0.049 0.03 0.998 14 3.7 63987 19.92
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 1.55 1.58 99.1 0.659 0.398 0.716 2.2 3.7 3167
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 4XGJ 1.55 27.919 1.34 63973 3247 98.99 0.1658 0.1645 0.1673 0.1909 0.1932 30.56
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 12.772 f_angle_d 1.269 f_chiral_restr 0.071 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing