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Structure and mechanism of a eukaryal nick-sealing RNA ligase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.285 α = 90 b = 55.285 β = 90 c = 102.545 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.000 NSLS X25
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 1.69 20 99.9 0.051 31.9 4.9 38947
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) 1 1.69 1.75 99.7 0.414 2.51 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.69 19.61 36965 1950 99.79 0.16046 0.15834 0.19953 0.2054 RANDOM 27.614
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 15.658 r_long_range_B_refined 7.278 r_long_range_B_other 6.966 r_dihedral_angle_1_deg 6.595 r_scangle_other 5.419 r_scbond_it 3.736 r_scbond_other 3.735 r_mcangle_it 3.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 15.658 r_long_range_B_refined 7.278 r_long_range_B_other 6.966 r_dihedral_angle_1_deg 6.595 r_scangle_other 5.419 r_scbond_it 3.736 r_scbond_other 3.735 r_mcangle_it 3.064 r_mcangle_other 3.063 r_mcbond_it 2.357 r_mcbond_other 2.357 r_angle_refined_deg 2.183 r_angle_other_deg 1.197 r_chiral_restr 0.176 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2717 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing