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Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Unknown
Crystal Properties Matthews coefficient Solvent content 1.86 33.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.989 α = 90 b = 76.989 β = 90 c = 45.84 γ = 120
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 SBC-3 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97931 APS 19-BM
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 1.65 50 98.8 0.061 0.067 0.026 0.996 31.7 6.2 36195 22.5
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 1.65 1.68 85.9 0.295 0.322 0.15 0.912 5.7 4.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 26.961 36102 1725 98.575 0.156 0.1544 0.1581 0.1775 0.185 30.315
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] -5.363 -5.363 10.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.797 r_dihedral_angle_3_deg 12.461 r_lrange_other 10.931 r_lrange_it 10.921 r_scangle_it 9.472 r_scangle_other 9.469 r_mcangle_it 8.427 r_mcangle_other 8.424 r_rigid_bond_restr 8.101 r_scbond_it 7.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.797 r_dihedral_angle_3_deg 12.461 r_lrange_other 10.931 r_lrange_it 10.921 r_scangle_it 9.472 r_scangle_other 9.469 r_mcangle_it 8.427 r_mcangle_other 8.424 r_rigid_bond_restr 8.101 r_scbond_it 7.44 r_scbond_other 7.437 r_mcbond_it 6.583 r_mcbond_other 6.578 r_dihedral_angle_1_deg 5.159 r_dihedral_angle_2_deg 2.061 r_angle_refined_deg 1.488 r_angle_other_deg 0.725 r_nbd_other 0.258 r_symmetry_nbd_other 0.22 r_nbd_refined 0.199 r_nbtor_refined 0.179 r_metal_ion_refined 0.119 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbd_refined 0.087 r_symmetry_nbtor_other 0.082 r_xyhbond_nbd_refined 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2392 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing