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Structure of phosphotransferase enzyme II, A component from Yersinia pestis CO92 at 1.2 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 2.5 M NH4 Sulphate, 0.1M Bis-Tris propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.906 α = 90 b = 57.946 β = 90 c = 78.742 γ = 90
Symmetry Space Group P 21 21 21
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 MIRROR 2010-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.961070 APS 21-ID-D
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 1.2 30 100 0.059 23.12 5.9 81918 81918 -3 16.1
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) 1.2 1.22 100 0.66 2.2 4.7
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 SAD THROUGHOUT 1.2 46.67 77534 77534 4096 99.59 0.14843 0.14679 0.1465 0.17861 0.1724 RANDOM 10.718
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] 0.15 0.02 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 19.771 r_dihedral_angle_3_deg 10.352 r_scangle_it 6.14 r_dihedral_angle_1_deg 5.929 r_scbond_it 4.198 r_mcangle_it 2.805 r_mcbond_it 1.902 r_angle_refined_deg 1.718 r_rigid_bond_restr 1.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 19.771 r_dihedral_angle_3_deg 10.352 r_scangle_it 6.14 r_dihedral_angle_1_deg 5.929 r_scbond_it 4.198 r_mcangle_it 2.805 r_mcbond_it 1.902 r_angle_refined_deg 1.718 r_rigid_bond_restr 1.635 r_angle_other_deg 1.054 r_mcbond_other 0.673 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 16
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building CCP4 model building MrBUMP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing CCP4 phasing