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Crystal structures of nuclease-ColE7 complexed with octamer DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 2.5 mM EDTA, 12.5 mM Tris-HCl (pH 7.5), 0.1 M Ammonium Formate, and 10 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.43 α = 90 b = 46.47 β = 90.39 c = 78.45 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 120 CCD ADSC QUANTUM 4 2003-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 SPring-8 BL12B2
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 2.5 40 96.6 0.045 36.4 4.07 15076 32.2
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 2.49 2.58 84.4 0.241 7.8
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 (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 7CEI 2.5 27.73 14389 14389 1455 95.3 0.216 0.216 0.2154 0.289 0.2878 RANDOM 44.9
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] 5.81 -0.96 9.19 -15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_improper_angle_d 4.83 c_scangle_it 3.26 c_mcangle_it 2.46 c_scbond_it 2.08 c_mcbond_it 1.46 c_angle_deg 1.3 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_improper_angle_d 4.83 c_scangle_it 3.26 c_mcangle_it 2.46 c_scbond_it 2.08 c_mcbond_it 1.46 c_angle_deg 1.3 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms 966 Solvent Atoms 232 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing