☰ Navigation Tabs
Crystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 28% MPD, 25 mM Potassium Phosphate
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.875 α = 90 b = 60.382 β = 94.06 c = 38.196 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 110 CCD AGILENT ATLAS CCD 2022-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.95 20.11 99.9 0.016 0.049 53.8 16 10282
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 100 0.148 0.305 5.85
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 1.95 19.18 9777 489 99.89 0.17308 0.17133 0.1818 0.20829 0.218 RANDOM 36.257
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] -2.48 0.08 -0.54 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.277 r_dihedral_angle_2_deg 7.496 r_dihedral_angle_1_deg 6.109 r_long_range_B_refined 5.962 r_long_range_B_other 5.844 r_scangle_other 3.251 r_scbond_it 2.185 r_scbond_other 2.183 r_angle_refined_deg 1.776 r_mcangle_other 1.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.277 r_dihedral_angle_2_deg 7.496 r_dihedral_angle_1_deg 6.109 r_long_range_B_refined 5.962 r_long_range_B_other 5.844 r_scangle_other 3.251 r_scbond_it 2.185 r_scbond_other 2.183 r_angle_refined_deg 1.776 r_mcangle_other 1.484 r_mcangle_it 1.481 r_mcbond_it 0.963 r_mcbond_other 0.954 r_angle_other_deg 0.59 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1037 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling CrysalisPro data reduction PHASER phasing