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Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 potassium thiocyanate, PEG MME 2000, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.7 α = 90 b = 69.424 β = 116.77 c = 66.293 γ = 90
Symmetry Space Group P 1 2 1
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 SBC-2 mirrors 2003-12-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD SBC-3 mirrors 2004-02-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 19-BM 0.9793, 0.9794, 0.956 APS 19-BM
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 1,2 1.6 23.9 95.2 0.069 8.6 4.1 64041 60955
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) 1,2 1.6 1.66 91.7 0.347 2.9 3.2
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 MAD THROUGHOUT 1.6 23.9 51951 51951 5905 94.92 0.22355 0.22355 0.21904 0.2186 0.26351 0.2638 RANDOM 26.621
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] -1.24 1.22 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.347 r_dihedral_angle_4_deg 19.442 r_dihedral_angle_3_deg 16.723 r_dihedral_angle_1_deg 5.301 r_scangle_it 4.238 r_scbond_it 2.62 r_mcangle_it 1.789 r_angle_refined_deg 1.417 r_mcbond_it 0.985 r_symmetry_vdw_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.347 r_dihedral_angle_4_deg 19.442 r_dihedral_angle_3_deg 16.723 r_dihedral_angle_1_deg 5.301 r_scangle_it 4.238 r_scbond_it 2.62 r_mcangle_it 1.789 r_angle_refined_deg 1.417 r_mcbond_it 0.985 r_symmetry_vdw_refined 0.323 r_symmetry_hbond_refined 0.32 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3295 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing