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Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 2.2M ammonium sulfate, 0.05M sodium citrate, pH 5.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.593 α = 90 b = 91.593 β = 90 c = 193.643 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2003-05-13 M SINGLE WAVELENGTH 2 1 100 CCD 2003-06-18
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A 2 ROTATING ANODE RIGAKU
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 2.06 72.55 97.8 0.062 36.9 3.7 19290
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 2.05 2.12 99.9 0.259 5.6 3.7 1965
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 MIR THROUGHOUT 2.06 72.55 18302 986 97.47 0.20372 0.20165 0.2009 0.24259 0.238 RANDOM 39.012
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] 0.95 0.48 0.95 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.469 r_dihedral_angle_4_deg 18.345 r_dihedral_angle_3_deg 15.409 r_dihedral_angle_1_deg 5.294 r_scangle_it 4.175 r_scbond_it 2.975 r_mcangle_it 1.983 r_angle_refined_deg 1.506 r_mcbond_it 1.444 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.469 r_dihedral_angle_4_deg 18.345 r_dihedral_angle_3_deg 15.409 r_dihedral_angle_1_deg 5.294 r_scangle_it 4.175 r_scbond_it 2.975 r_mcangle_it 1.983 r_angle_refined_deg 1.506 r_mcbond_it 1.444 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.206 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.198 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1643 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing