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The C-terminal loop of the homing endonuclease I-CreI is essential for DNA binding and cleavage. Identification of a novel site for specificity engineering in the I-CreI scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.088 α = 90 b = 69.088 β = 90 c = 93.04 γ = 90
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 4 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 ESRF ID14-4 2 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 93.2 25943 25943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1g9z 2 34.54 25943 1380 93.2 0.18634 0.18379 0.23464 RANDOM 34.251
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] -0.09 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_dihedral_angle_4_deg 25.029 r_dihedral_angle_3_deg 16.413 r_scangle_it 6.049 r_dihedral_angle_1_deg 5.743 r_scbond_it 4.091 r_mcangle_it 2.702 r_angle_refined_deg 2.137 r_mcbond_it 1.785 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_dihedral_angle_4_deg 25.029 r_dihedral_angle_3_deg 16.413 r_scangle_it 6.049 r_dihedral_angle_1_deg 5.743 r_scbond_it 4.091 r_mcangle_it 2.702 r_angle_refined_deg 2.137 r_mcbond_it 1.785 r_nbtor_refined 0.318 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.172 r_symmetry_vdw_refined 0.165 r_bond_refined_d 0.029 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2484 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement