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Crystal structure of E.coli LigT complexed with 3'-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LDI PDBid: 5ldi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 18% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.41 α = 90 b = 88.35 β = 114.95 c = 73.97 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 MAR CCD 165 mm 2013-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 30 99.3 0.092 0.996 14.11 3.8 19216 46.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.82 97.8 0.804 0.629 1.76 3.76
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 PDBid: 5ldi 2.752 28.746 1.99 19194 1922 99.61 0.2164 0.2117 0.213 0.2587 0.2576 Random selection 48.21
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 11.856 f_angle_d 0.83 f_chiral_restr 0.032 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5449 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing