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Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.04 69.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.14 α = 90 b = 75.14 β = 90 c = 181.81 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD CUSTOM-MADE 2002-09-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.978795, 0.978462, 0.950037 NSLS X12C
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 2 50 95.1 0.053 38.3 12.8 34611 36112 14.9
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) 2 2.07 69.6 0.133 9.2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 39.95 36112 32009 1573 88.5 0.219 0.2195 0.232 0.2188 RANDOM 35.9
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] 6.82 6.82 -13.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 3.71 c_scbond_it 2.77 c_mcangle_it 2.07 c_mcbond_it 1.39 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing CNS refinement