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Crystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Ca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9Y PDB ENTRY 1G9Y
Crystallization Crystal Properties Matthews coefficient Solvent content 2.39 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.179 α = 90 b = 94.21 β = 104.83 c = 51.34 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 100 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.6 47.1 99 0.12 7 3.5 14572 2 33.18
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 2.6 2.74 100 0.48 3.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1G9Y 2.6 47.105 1.26 14548 2722 96.64 0.1685 0.1614 0.1647 0.2331
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.899 f_angle_d 1.2 f_chiral_restr 0.047 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms 978 Solvent Atoms 86 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing