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Endoribonuclease in complex with its cognate antitoxin from Mycobacterial species
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.0, 20% (w/v) polyethylene glycol 3000
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.473 α = 90 b = 70.018 β = 113.28 c = 76.754 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 100 CCD ADSC QUANTUM 315r 2015-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97945 PAL/PLS 5C (4A)
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 2.3 30 95.21 30.21 4 23785
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 3SE5 2.3 30 23785 1268 95.21 0.2145 0.2117 0.2152 0.2666 0.2691 RANDOM 44.244
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] -0.02 -0.04 0.07 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 15.519 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.677 r_angle_other_deg 1.006 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.259 r_dihedral_angle_4_deg 17.922 r_dihedral_angle_3_deg 15.519 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.677 r_angle_other_deg 1.006 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4374 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing