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Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 2.0M Ammonium sulfate, 0.1M Sodium acetate tri-hydrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.514 α = 114.462 b = 65.648 β = 111.89 c = 71.802 γ = 90.01
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 315r 2013-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.798 50 97.1 0.055 26.33 2.3 73010
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 1.8 1.86 0.261
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.798 33.529 73009 3707 96.79 0.188 0.1853 0.1939 0.231 0.2388 24.683
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] 0.002 -0.001 0.001 -0.011 0.002 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.153 r_dihedral_angle_6_deg 16.158 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 7.146 r_lrange_it 6.732 r_lrange_other 6.722 r_scangle_it 4.639 r_scangle_other 4.639 r_mcangle_other 3.434 r_mcangle_it 3.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.153 r_dihedral_angle_6_deg 16.158 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 7.146 r_lrange_it 6.732 r_lrange_other 6.722 r_scangle_it 4.639 r_scangle_other 4.639 r_mcangle_other 3.434 r_mcangle_it 3.433 r_scbond_it 3.049 r_scbond_other 3.048 r_mcbond_it 2.353 r_mcbond_other 2.341 r_angle_refined_deg 1.568 r_angle_other_deg 0.519 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.234 r_nbd_other 0.231 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6288 Nucleic Acid Atoms 531 Solvent Atoms 349 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing