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Crystal structure of intein homing endonuclease II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SEMET PI-TkoII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Ammonium sulfate, Sodium phosphate, Sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.58 72.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.7 α = 90 b = 149.06 β = 90 c = 146.13 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 2.7 40 93.2 0.046 13.4 3.9 30434 30434 1.7 13.2
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 2.7 2.8 79.5 0.253 1.7
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 SEMET PI-TkoII 2.7 38.39 30427 30416 1512 93.2 0.206 0.206 0.2046 0.243 0.2425 RANDOM 58.6
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] 5.08 1.94 -7.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 3.41 c_mcangle_it 2.64 c_scbond_it 2.03 c_mcbond_it 1.48 c_angle_deg 1.3 c_improper_angle_d 0.72 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 3.41 c_mcangle_it 2.64 c_scbond_it 2.03 c_mcbond_it 1.48 c_angle_deg 1.3 c_improper_angle_d 0.72 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4392 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 15
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing