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Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 300 100mM Hepes
25% (v/v) Jeffamine M-600
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.969 α = 90 b = 60.364 β = 116.47 c = 107.085 γ = 90
Symmetry Space Group C 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 PIXEL DECTRIS EIGER2 XE 16M 2019-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.84 53.56 97.1 0.044 0.053 0.029 0.995 11.3 3.2 93596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.89 74.5 0.724 0.913 0.547 0.739 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3wzi 1.84 53.56 88795 4770 96.88 0.1947 0.1924 0.2372 0.2319 RANDOM 34.154
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] 0.43 -2.95 -0.45 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.42 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 7.356 r_angle_refined_deg 1.623 r_angle_other_deg 1.257 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.42 r_dihedral_angle_4_deg 17.457 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 7.356 r_angle_refined_deg 1.623 r_angle_other_deg 1.257 r_chiral_restr 0.073 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 7586 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing