☰ Navigation Tabs
Crystal structure of Staphylococcal nuclease variant Delta+PHS I72R at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQO RCSB entry 1tqo, all waters removed, b = 20.0, ILE-72 and ILE-92 truncated to ALA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.181 α = 90 b = 60.425 β = 90 c = 73.124 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 CCD BRUKER APEX II multi-layer optics 2007-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 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 1.99 46.6 99.7 0.0215 0.0581 42.54 20.75 10315 10279 23.7
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 1.99 2.09 97.6 0.0965 0.2078 9.87 9.35 1358
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT RCSB entry 1tqo, all waters removed, b = 20.0, ILE-72 and ILE-92 truncated to ALA 1.99 1.99 10280 10218 1019 99.46 0.205 0.205 0.2 0.2069 0.258 RANDOM 13.049
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.072 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_1_deg 5.647 r_scangle_it 2.248 r_scbond_it 1.419 r_angle_refined_deg 1.226 r_mcangle_it 0.951 r_mcbond_it 0.641 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.072 r_dihedral_angle_3_deg 12.563 r_dihedral_angle_4_deg 12.517 r_dihedral_angle_1_deg 5.647 r_scangle_it 2.248 r_scbond_it 1.419 r_angle_refined_deg 1.226 r_mcangle_it 0.951 r_mcbond_it 0.641 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1045 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction