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Staphylococcus aureus endonuclease IV orthorhombic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XP3 1xp3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 - 0.1 M HEPES pH 7.0
- 2.2 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.857 α = 90 b = 82.581 β = 90 c = 105.091 γ = 90
Symmetry Space Group P 21 21 21
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 2021-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.800 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.05 52.545 99.1 0.063 1 14.2 7.2 156665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 95.8 1.882 0.319 0.5 6.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1xp3 1.05 52.545 156428 7783 98.942 0.137 0.1358 0.1282 0.1577 0.1499 15.324
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] -0.042 0.795 -0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_4_deg 16.411 r_dihedral_angle_3_deg 12.21 r_dihedral_angle_1_deg 6.01 r_lrange_it 4.006 r_lrange_other 2.993 r_scangle_it 2.187 r_scangle_other 1.978 r_scbond_it 1.685 r_angle_refined_deg 1.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_4_deg 16.411 r_dihedral_angle_3_deg 12.21 r_dihedral_angle_1_deg 6.01 r_lrange_it 4.006 r_lrange_other 2.993 r_scangle_it 2.187 r_scangle_other 1.978 r_scbond_it 1.685 r_angle_refined_deg 1.566 r_mcangle_it 1.566 r_mcangle_other 1.566 r_scbond_other 1.562 r_angle_other_deg 1.505 r_rigid_bond_restr 1.488 r_mcbond_it 1.126 r_mcbond_other 1.124 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.198 r_nbd_other 0.182 r_nbtor_refined 0.17 r_symmetry_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MoRDa phasing