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Crystal structure of Staphylococcal nuclease variant L25K at cryogenic temperature
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.978 α = 90 b = 60.282 β = 93.43 c = 37.961 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 2008-06-15 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 2.1 60.28 100 0.0816 0.0349 20.06 15.45 8220 8216 38.6
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 2.1 2.2 100 0.388 0.2114 4.49 11.86 1058
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 23.29 8181 8181 803 99.78 0.215 0.215 0.209 0.209 0.278 0.2773 RANDOM 31.224
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] -0.05 0.01 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.39 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_1_deg 7.064 r_scangle_it 3.985 r_scbond_it 2.636 r_mcangle_it 1.683 r_angle_refined_deg 1.216 r_mcbond_it 0.934 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.39 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_4_deg 14.772 r_dihedral_angle_1_deg 7.064 r_scangle_it 3.985 r_scbond_it 2.636 r_mcangle_it 1.683 r_angle_refined_deg 1.216 r_mcbond_it 0.934 r_chiral_restr 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 45 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