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Crystal Structure of the Nanoarchaeum equitans tRNA splicing endonuclease structural subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IEY PDB entry 3IEY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 303 0.10 M sodium acetate pH 4.6, 0.30 M ammonium acetate, 35% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 3.41 63.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.434 α = 90 b = 95.434 β = 90 c = 47.791 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 225 mm CCD 2009-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 100 100 0.097 0.097 10.5 19 13062 13062 2 8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.9 0.624 0.624 4.9 11.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3IEY 2.2 41.38 12345 643 99.84 0.24964 0.24827 0.2501 0.27712 0.2813 RANDOM 35.247
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] 0.39 0.2 0.39 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.093 r_dihedral_angle_3_deg 18.388 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_1_deg 5.836 r_scangle_it 2.853 r_scbond_it 1.747 r_angle_refined_deg 1.266 r_mcangle_it 1.206 r_mcbond_it 0.646 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.093 r_dihedral_angle_3_deg 18.388 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_1_deg 5.836 r_scangle_it 2.853 r_scbond_it 1.747 r_angle_refined_deg 1.266 r_mcangle_it 1.206 r_mcbond_it 0.646 r_chiral_restr 0.103 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1269 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection