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Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 ammonium sulfate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.43 72.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.441 α = 90 b = 145.441 β = 90 c = 82.484 γ = 120
Symmetry Space Group P 63 2 2
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 MARRESEARCH mirrors 2003-03-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.3 50 98.8 0.064 0.064 22.1 13 23332 23052 18.6
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 2.3 2.38 98.9 0.453 0.453 2.1
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 41.99 23373 22976 2268 98.3 0.233 0.233 0.275 RANDOM 56.5
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] -7.83 4.48 -7.83 15.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 9.14 c_scbond_it 7.06 c_mcangle_it 6.06 c_mcbond_it 4.41 c_angle_deg 1.6 c_improper_angle_d 0.9 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1981 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 15
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing