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The structure of a bacterial homing endonuclease : I-Ssp6803I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 15% to 20% MPD, 100 mM MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.67 73.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.777 α = 90 b = 143.777 β = 90 c = 319.179 γ = 90
Symmetry Space Group I 4 2 2
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 315 2006-06-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-08-25 M SINGLE WAVELENGTH 3 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V 2006-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.979 ALS 5.0.2 2 SYNCHROTRON ALS BEAMLINE 5.0.2 0.965 ALS 5.0.2 3 ROTATING ANODE RIGAKU RU200
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 1,2,3 3.1 160.13 94 0.083 10.7 7.6 28899
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) 1,2,3 3.1 3.15 61.4 0.374 7.6 928
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 3.1 160.13 28898 1459 93.96 0.281 0.278 0.2612 0.328 0.302 RANDOM 83.07
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] 3.44 3.44 -6.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_3_deg 19.415 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_1_deg 5.497 r_angle_refined_deg 1.889 r_scangle_it 1.158 r_mcangle_it 0.682 r_scbond_it 0.609 r_mcbond_it 0.374 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.079 r_dihedral_angle_3_deg 19.415 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_1_deg 5.497 r_angle_refined_deg 1.889 r_scangle_it 1.158 r_mcangle_it 0.682 r_scbond_it 0.609 r_mcbond_it 0.374 r_nbtor_refined 0.302 r_chiral_restr 0.228 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.14 r_metal_ion_refined 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4540 Nucleic Acid Atoms 1189 Solvent Atoms 16 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection