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Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 4000, potassium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.551 α = 90 b = 175.551 β = 90 c = 44.603 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 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000, 1.0082, 1.0089, 0.9 SPring-8 BL38B1
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 2.4 20 99.1 26765 26765
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.401 20 25421 25421 1343 98.84 0.257 0.257 0.255 0.2635 0.297 0.3017 RANDOM 52.495
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] 2.09 2.09 -4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.519 r_dihedral_angle_4_deg 20.469 r_dihedral_angle_3_deg 17.626 r_dihedral_angle_1_deg 5.785 r_angle_other_deg 3.845 r_scangle_it 2.643 r_scbond_it 1.686 r_angle_refined_deg 1.426 r_mcangle_it 1.272 r_mcbond_it 0.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.519 r_dihedral_angle_4_deg 20.469 r_dihedral_angle_3_deg 17.626 r_dihedral_angle_1_deg 5.785 r_angle_other_deg 3.845 r_scangle_it 2.643 r_scbond_it 1.686 r_angle_refined_deg 1.426 r_mcangle_it 1.272 r_mcbond_it 0.702 r_xyhbond_nbd_other 0.277 r_nbd_refined 0.211 r_symmetry_vdw_other 0.18 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.158 r_nbtor_other 0.115 r_symmetry_vdw_refined 0.105 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 4125 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SOLVE phasing REFMAC refinement HKL-2000 data reduction