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RNA ligase RtcB/Mn2+ complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 1.5 M (NH4)2SO4, 75 mM NaCl, and 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.34 63.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.081 α = 90 b = 84.899 β = 115.65 c = 124.2 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD APEX II CCD 2011-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.55 50 95 310153 294058 2 1
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 1.54 1.61 62.5
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 (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1.48 46.74 310153 294058 15653 87.65 0.14365 0.14365 0.14183 0.1387 0.17794 0.1746 RANDOM 30.239
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] -1.83 -1.33 1.55 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.033 r_dihedral_angle_4_deg 17.286 r_dihedral_angle_3_deg 14.035 r_scangle_it 8.775 r_scbond_it 6.477 r_dihedral_angle_1_deg 5.944 r_mcangle_it 5.618 r_mcbond_it 4.048 r_rigid_bond_restr 2.193 r_angle_refined_deg 1.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.033 r_dihedral_angle_4_deg 17.286 r_dihedral_angle_3_deg 14.035 r_scangle_it 8.775 r_scbond_it 6.477 r_dihedral_angle_1_deg 5.944 r_mcangle_it 5.618 r_mcbond_it 4.048 r_rigid_bond_restr 2.193 r_angle_refined_deg 1.316 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11340 Nucleic Acid Atoms Solvent Atoms 1654 Heterogen Atoms 180
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling