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Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 287 1M ammonium sulphate, 0.1M BICINE, pH8.8, VAPOR DIFFUSION, HANGING DROP, temperature 287K 2 VAPOR DIFFUSION, HANGING DROP 8 287 1M ammonium sulphate, 0.1M Tris-HCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.671 α = 90 b = 119.777 β = 105.63 c = 44.492 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 ADSC QUANTUM 315 2007-11-12 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2007-08-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.92 Diamond I03 2 SYNCHROTRON ESRF BEAMLINE BM14 0.97866, 0.97893, 0.88560 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.4 59.888 87.9 0.077 0.077 6.8 3.4 75030 74121 6 6 10.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.48 75.8 0.307 0.307 2.1 1.8 9314
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 1.4 41.094 75030 71146 3514 84.38 0.1599 0.159 0.1582 0.189 0.1884 RANDOM 16.31
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] 2.247 -1.426 -1.65 -0.596
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.428 f_nbd_refined 4.114 f_angle_d 1.33 f_chiral_restr 0.083 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3614 Nucleic Acid Atoms Solvent Atoms 680 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing SHELX phasing PHENIX refinement PDB_EXTRACT data extraction MxCuBE data collection SHELXCD phasing SHELXE model building