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Structure of bifunctional endonuclease (AtBFN2) in complex with phosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CWM PDB ENTRY 4CWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES, PH 7.5 0.2 M NA2HPO4 30% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.524 α = 71.34 b = 52.87 β = 78.63 c = 60.841 γ = 76.62
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 MARRESEARCH MX-300 MIRRORS 2013-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 NSRRC BL15A1
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 25 96.7 0.07 9.4 2 34563 -3
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 2.07 95.2 0.26 3.3 2
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 4CWM 2 25.43 31321 1659 94.09 0.20423 0.20184 0.2068 0.24942 0.2527 RANDOM 28.36
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] -17.54 11 0.19 26.73 15.7 -9.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 15.369 r_dihedral_angle_4_deg 10.685 r_dihedral_angle_1_deg 5.848 r_mcangle_it 2.459 r_scbond_it 1.945 r_mcbond_it 1.677 r_mcbond_other 1.676 r_angle_refined_deg 1.563 r_angle_other_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 15.369 r_dihedral_angle_4_deg 10.685 r_dihedral_angle_1_deg 5.848 r_mcangle_it 2.459 r_scbond_it 1.945 r_mcbond_it 1.677 r_mcbond_other 1.676 r_angle_refined_deg 1.563 r_angle_other_deg 0.915 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4064 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 247
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing