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AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Morpheus screen H1 conditions: 0.02 M of L-Na-glutamate, alanine (racemic), glycine, lysine HCl (racemic), serine (racemic), 0.1 M buffer (1 M Imidazole, 1 M MES, pH 6.5), 30% precipitant (20% w/v PEG 20 000, 40% v/v PEG MME 550)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.129 α = 90 b = 116.21 β = 102.91 c = 56.774 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 PIXEL DECTRIS PILATUS 6M 2019-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.9 40.07 98.5 0.081 0.094 0.998 10.55 3.8 36585 36.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 97.6 0.807 0.943 0.615 1.43 3.7
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 6G3B 1.9 40.07 34760 1825 98.59 0.17826 0.17621 0.1829 0.21671 0.2218 RANDOM 35.854
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] -0.72 -0.35 -1.27 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.952 r_dihedral_angle_4_deg 16.556 r_dihedral_angle_3_deg 15.314 r_long_range_B_refined 5.562 r_long_range_B_other 5.368 r_dihedral_angle_1_deg 5.159 r_scangle_other 3.118 r_mcangle_other 2.856 r_mcangle_it 2.855 r_scbond_it 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.952 r_dihedral_angle_4_deg 16.556 r_dihedral_angle_3_deg 15.314 r_long_range_B_refined 5.562 r_long_range_B_other 5.368 r_dihedral_angle_1_deg 5.159 r_scangle_other 3.118 r_mcangle_other 2.856 r_mcangle_it 2.855 r_scbond_it 1.874 r_scbond_other 1.868 r_mcbond_it 1.775 r_mcbond_other 1.771 r_angle_refined_deg 1.227 r_angle_other_deg 0.998 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3720 Nucleic Acid Atoms 893 Solvent Atoms 487 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling BALBES phasing ARP/wARP model building Coot model building