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Crystal structure of Staphylococcal nuclease variant Delta+PHS 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, and E92A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 17% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.097 α = 90 b = 60.651 β = 94.44 c = 36.948 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 BRUKER APEX II multi-layer optics 2007-09-05 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 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 1.8 31.5 99.37 0.152 51.898 13.18 14206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 100 0.415 6.22 7.86
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 (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, and E92A 1.8 31.01 12767 10735 1179 93.32 0.19556 0.1895 0.1889 0.2512 0.2495 RANDOM 22.944
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 34.112 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 9.345 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.785 r_scbond_it 2.535 r_angle_refined_deg 1.772 r_mcangle_it 1.629 r_mcbond_it 1.11 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.112 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 9.345 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.785 r_scbond_it 2.535 r_angle_refined_deg 1.772 r_mcangle_it 1.629 r_mcbond_it 1.11 r_nbtor_refined 0.31 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.121 r_symmetry_vdw_refined 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 106 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