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Crystal structure of a truncated tRNA, TPHE39A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 40% MPD, 0.1M HEPES, 0.2M Sodium Chloride, 0.2M Calcium acetate, pH7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.366 α = 90 b = 62.366 β = 90 c = 115.2 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 210 mirrors 2008-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.70 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 50 94.1 0.076 23.9 15.3 13064 13064 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 90.3 0.276 12.7 14.7 246
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 SAD THROUGHOUT 1.75 27.42 12408 641 93.22 0.2086 0.207 0.2033 0.24037 0.2327 RANDOM 25.072
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] 0.41 0.2 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.358 r_angle_refined_deg 1.213 r_scbond_it 0.831 r_nbtor_refined 0.267 r_nbd_refined 0.154 r_symmetry_vdw_refined 0.131 r_metal_ion_refined 0.113 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.102 r_symmetry_metal_ion_refined 0.089
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.358 r_angle_refined_deg 1.213 r_scbond_it 0.831 r_nbtor_refined 0.267 r_nbd_refined 0.154 r_symmetry_vdw_refined 0.131 r_metal_ion_refined 0.113 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.102 r_symmetry_metal_ion_refined 0.089 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 813 Solvent Atoms 161 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHELXE model building