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Crystal structure of the E.coli pseudouridine synthase TruD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 magnesium chloride, Hepes 7.5, isopropanol, PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.25 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.665 α = 90 b = 108.78 β = 90 c = 111.855 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 IMAGE PLATE RIGAKU RAXIS IV 2003-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.2 27.69 97.8 0.07 0.07 43.1 10.76 39254 3 28.8
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) 1 2.2 2.28 99.6 0.414 0.414 7.2 10.15
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 SIR THROUGHOUT 2.2 27.69 39254 39254 3938 97.6 0.216 0.216 0.2203 0.254 0.2591 RANDOM 40.9
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] 3.07 5.02 -8.09
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.32 c_mcangle_it 2.32 c_scbond_it 2.26 c_mcbond_it 1.49 c_angle_deg 1.2 c_improper_angle_d 0.66 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 3.32 c_mcangle_it 2.32 c_scbond_it 2.26 c_mcbond_it 1.49 c_angle_deg 1.2 c_improper_angle_d 0.66 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5338 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 41
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing