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Crystal structure of tRNase Z from Thermotoga maritima
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.902 α = 90 b = 73.642 β = 90 c = 91.994 γ = 90
Symmetry Space Group P 21 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 100 CCD MARRESEARCH 2004-07-11 M SINGLE WAVELENGTH
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) 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 2.6 50 98.8 5.7 24096 23807 37.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 97.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 Crystal 1: single wavelength protocol, Crystal 2: Mad protocol THROUGHOUT 2.6 47.8 23789 1141 98.9 0.225 0.225 0.2238 0.279 0.2801 RANDOM 68.1
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] 7.82 0.71 -8.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 7.65 c_mcangle_it 5.96 c_scbond_it 5.59 c_mcbond_it 3.91 c_angle_deg 1.4 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 7.65 c_mcangle_it 5.96 c_scbond_it 5.59 c_mcbond_it 3.91 c_angle_deg 1.4 c_improper_angle_d 0.84 c_bond_d 0.008 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 4004 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing