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AvaII restriction endonuclease in the absence of nucleic acids
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 0.03 M CaCl2, 0.1 M MES/imidazole, pH 6.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 (Morpheus screen A4 condition with MgCl2 eliminated).
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.231 α = 90 b = 102.733 β = 90.67 c = 121.197 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 EIGER X 16M 2019-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.35 53.3 99.9 0.099 0.119 0.065 0.99 5.5 3.3 37373 54
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 2.35 2.43 99.8 0.452 0.55 0.309 0.764 1.8 3.1
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 2.32 51.37 35320 1958 96.37 0.21848 0.21634 0.2116 0.25827 0.2578 RANDOM 71.422
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] 16.22 7.04 -30.14 13.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.71 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 14.925 r_long_range_B_refined 6.525 r_long_range_B_other 6.496 r_dihedral_angle_1_deg 5.581 r_mcangle_it 4.406 r_mcangle_other 4.405 r_scangle_other 4.105 r_mcbond_it 2.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.71 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 14.925 r_long_range_B_refined 6.525 r_long_range_B_other 6.496 r_dihedral_angle_1_deg 5.581 r_mcangle_it 4.406 r_mcangle_other 4.405 r_scangle_other 4.105 r_mcbond_it 2.825 r_mcbond_other 2.825 r_scbond_it 2.547 r_scbond_other 2.547 r_angle_refined_deg 1.141 r_angle_other_deg 0.886 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 7252 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing ARP/wARP model building