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Crystal structure of the HEPN family member AbiV, an RNase in a two-component antiphage system in Lactococcus lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 1.0M Lithium chloride, 0.1M Sodium acetate, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.173 α = 90 b = 144.955 β = 95.53 c = 55.563 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 MARRESEARCH 2016-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 2.92 144.96 99.2 0.134 0.156 0.08 0.995 8.6 3.8 18073
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 2.92 3.08 99.8 0.948 1.099 0.555 0.676 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.92 72.48 17157 889 99.13 0.2102 0.20799 0.2136 0.25364 0.2561 RANDOM 74.413
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] 0.81 -4.6 -0.03 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.03 r_dihedral_angle_4_deg 25.145 r_dihedral_angle_3_deg 22.792 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_dihedral_angle_1_deg 6.664 r_mcangle_it 4.573 r_mcangle_other 4.572 r_scangle_other 4.221 r_mcbond_it 2.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.03 r_dihedral_angle_4_deg 25.145 r_dihedral_angle_3_deg 22.792 r_long_range_B_refined 6.946 r_long_range_B_other 6.946 r_dihedral_angle_1_deg 6.664 r_mcangle_it 4.573 r_mcangle_other 4.572 r_scangle_other 4.221 r_mcbond_it 2.746 r_mcbond_other 2.745 r_scbond_it 2.471 r_scbond_other 2.47 r_angle_refined_deg 1.777 r_angle_other_deg 1.319 r_chiral_restr 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 5350 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing