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Crystal structure of Staphylococcal nuclease variant Delta+PHS V104K at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQO 1TQO.PDB where all waters removed, all Bs=20.0 A^2, V104A, and E92A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 40% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.079 α = 90 b = 60.518 β = 93.064 c = 38.22 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 BRUKER APEX II multi-layer optics 2007-06-20 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 2 21.88 100 0.0761 0.0364 19.51 13.42 9648 9646 34.2
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) 2 2.1 100 0.4489 0.3477 2.8 6.29 1307
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TQO.PDB where all waters removed, all Bs=20.0 A^2, V104A, and E92A 2 21.88 9617 8525 853 88.65 0.211 0.216 0.211 0.2137 0.261 0.2605 RANDOM 29.683
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 0.02 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 17.661 r_dihedral_angle_3_deg 15.809 r_dihedral_angle_1_deg 6.148 r_scangle_it 3.336 r_scbond_it 2.157 r_angle_refined_deg 1.914 r_mcangle_it 1.497 r_mcbond_it 0.912 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 17.661 r_dihedral_angle_3_deg 15.809 r_dihedral_angle_1_deg 6.148 r_scangle_it 3.336 r_scbond_it 2.157 r_angle_refined_deg 1.914 r_mcangle_it 1.497 r_mcbond_it 0.912 r_nbtor_refined 0.308 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 54 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