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Crystal structure of Staphylococcal nuclease variant D+PHS/V23E at pH 6 determined at 100 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC 3BDC WITH NON-PROTEIN ATOMS REMOVED, B-FACTORS SET TO 20 AND RESIDUES 23,113-116 CHANGED TO ALA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 277 22% MPD, 25 mM Potassium Phosphate, pdTp, CaCl2, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.033 α = 90 b = 60.453 β = 94.44 c = 37.626 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 APEX II CCD MULTI-LAYER OPTICS 2009-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 37.51 99.6 0.0365 41.19 12.13 11002 29.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.7 0.2139 5.68 5.21
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 3BDC WITH NON-PROTEIN ATOMS REMOVED, B-FACTORS SET TO 20 AND RESIDUES 23,113-116 CHANGED TO ALA 1.9 37.51 10474 10474 528 100 0.189 0.187 0.1877 0.227 0.2274 RANDOM 41.46
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] -0.12 0.15 -0.02 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_3_deg 16.444 r_dihedral_angle_4_deg 6.915 r_dihedral_angle_1_deg 6.546 r_scangle_it 5.523 r_scbond_it 3.518 r_mcangle_it 2.522 r_angle_refined_deg 1.695 r_mcbond_it 1.467 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_3_deg 16.444 r_dihedral_angle_4_deg 6.915 r_dihedral_angle_1_deg 6.546 r_scangle_it 5.523 r_scbond_it 3.518 r_mcangle_it 2.522 r_angle_refined_deg 1.695 r_mcbond_it 1.467 r_chiral_restr 0.133 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1035 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 26
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement SAINT data reduction XPREP data reduction