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Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 293 Ammonium sulfate, PEG 200, sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.651 α = 90 b = 78.652 β = 91.97 c = 32.901 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 ADSC QUANTUM 4 2002-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.071 SSRL BL1-5
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 1.75 40 99.7 0.045 39.1 7.2 253851 253092
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) 1.755 1.8 99.1 0.515 3.2
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.755 34.71 35113 33364 1749 99.3 0.18438 0.18438 0.18201 0.22926 RANDOM 18.498
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] 0.78 -0.9 0.07 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.836 r_scangle_it 4.2 r_scbond_it 2.833 r_mcangle_it 2.393 r_angle_refined_deg 1.897 r_mcbond_it 1.398 r_angle_other_deg 0.932 r_symmetry_vdw_other 0.308 r_nbd_other 0.263 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.836 r_scangle_it 4.2 r_scbond_it 2.833 r_mcangle_it 2.393 r_angle_refined_deg 1.897 r_mcbond_it 1.398 r_angle_other_deg 0.932 r_symmetry_vdw_other 0.308 r_nbd_other 0.263 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.126 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.12 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2748 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing