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Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 2.0 M Ammonium Sulfate, 100 mM MES, 20 mM NaCl, 10 mM CaCl2, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.89 α = 90 b = 81.712 β = 99.51 c = 73.583 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.5000 ALS 8.2.1
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 2.5 50 97.7 0.055 14.2 6.9 29547
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 2.5 2.59 82.2 0.277 5 2457
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 THROUGHOUT 2.5 50 29363 1483 97.74 0.226 0.223 0.2239 0.277 0.2781 RANDOM 66.001
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] -1.59 -1.63 2.04 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 17.067 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_1_deg 5.03 r_angle_refined_deg 1.094 r_scangle_it 0.582 r_scbond_it 0.356 r_nbtor_refined 0.295 r_mcangle_it 0.261 r_xyhbond_nbd_refined 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.118 r_dihedral_angle_4_deg 17.067 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_1_deg 5.03 r_angle_refined_deg 1.094 r_scangle_it 0.582 r_scbond_it 0.356 r_nbtor_refined 0.295 r_mcangle_it 0.261 r_xyhbond_nbd_refined 0.187 r_nbd_refined 0.172 r_mcbond_it 0.148 r_chiral_restr 0.085 r_symmetry_vdw_refined 0.071 r_symmetry_hbond_refined 0.011 r_metal_ion_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5438 Nucleic Acid Atoms 896 Solvent Atoms 168 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction