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The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 279 0.1M NaCl, 0.1M Bis Tris pH6.5,
1.5M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.77 α = 90 b = 65.849 β = 90 c = 68.917 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 ADSC QUANTUM 210r 2009-07-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97950, 0.97992 APS 19-BM
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 1.7 50 99.9 0.058 10.1 7.2 33607 33607 -3 24.2
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 1.7 1.73 100 0.477 6.6 1674
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 MAD THROUGHOUT 1.7 29.42 33552 33552 1701 99.91 0.168 0.168 0.166 0.1736 0.199 0.2037 RANDOM 22.025
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] -1.23 -2.24 3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.469 r_dihedral_angle_4_deg 22.964 r_dihedral_angle_3_deg 11.925 r_dihedral_angle_1_deg 5.762 r_scangle_it 3.404 r_scbond_it 2.088 r_mcangle_it 1.454 r_angle_refined_deg 1.382 r_angle_other_deg 0.898 r_mcbond_it 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.469 r_dihedral_angle_4_deg 22.964 r_dihedral_angle_3_deg 11.925 r_dihedral_angle_1_deg 5.762 r_scangle_it 3.404 r_scbond_it 2.088 r_mcangle_it 1.454 r_angle_refined_deg 1.382 r_angle_other_deg 0.898 r_mcbond_it 0.862 r_mcbond_other 0.261 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building