☰ Navigation Tabs
RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ODI pdb entry 2ODI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 0.02 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, 30% (V/V) 2-METHYL-2,4-PENTANEDIOL , pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.354 α = 90 b = 87.551 β = 90 c = 79.162 γ = 90
Symmetry Space Group P 21 21 2
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 BENT MIRROR 2006-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 30 99.9 0.079 5.8 3.2 57635 57635 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 100 0.26 2.9 3.2 8336
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 (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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2ODI 1.75 29.72 57579 57579 2882 99.8 0.176 0.176 0.174 0.1837 0.213 0.2196 RANDOM 8.32
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] 0.2 0.68 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 18.347 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_1_deg 6.688 r_scangle_it 2.237 r_scbond_it 1.8 r_angle_refined_deg 1.35 r_mcangle_it 1.032 r_angle_other_deg 0.911 r_mcbond_it 0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.949 r_dihedral_angle_4_deg 18.347 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_1_deg 6.688 r_scangle_it 2.237 r_scbond_it 1.8 r_angle_refined_deg 1.35 r_mcangle_it 1.032 r_angle_other_deg 0.911 r_mcbond_it 0.799 r_symmetry_vdw_other 0.267 r_symmetry_vdw_refined 0.224 r_nbd_other 0.209 r_nbd_refined 0.199 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.18 r_mcbond_other 0.166 r_xyhbond_nbd_refined 0.161 r_metal_ion_refined 0.151 r_nbtor_other 0.079 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3844 Nucleic Acid Atoms 890 Solvent Atoms 645 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling