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Crystal Structure of UPF0341 Protein (yhiQ) from Shigella flexneri in complex with S-Adenosyl Homocysteine, Northeast Structural Genomics Target SfR275
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 8.5 291 100mM Tris-HCl pH 8.5, 8% PEG 8000, 50 mM NaCl, 5 mM DTT, 5 mM SAM, MICROBATCH UNDER OIL, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.403 α = 90 b = 74.737 β = 90 c = 79.423 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 ADSC QUANTUM 4 mirrors 2007-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97911 NSLS X4A
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 37.41 98.3 0.08 0.064 19.81 6 32699 32699 5.8
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) 2 2.07 100 0.258 0.246 8.51 6.3 3288
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2 37.41 2 2 32699 30301 2946 92 0.214 0.213 0.213 0.229 0.23 0.2436 RANDOM 17.1
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] 4.85 -1.15 -3.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_improper_angle_d 1.5 c_angle_deg 1.4 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_improper_angle_d 1.5 c_angle_deg 1.4 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 26
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SnB phasing SOLVE phasing RESOLVE phasing XTALVIEW refinement