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Crystal structure of N-ColE7/12-bp DNA/Zn complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PT3 PDB ENTRY 1PT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25mM Tris-HCl, 0.1M Ammonium chloride, 10.5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.19 α = 90 b = 44.19 β = 90 c = 203.97 γ = 90
Symmetry Space Group P 41 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 120 IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 98 0.045 41.1 11.7 89323 7597 38.7
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 2.5 2.59 99.5 0.151 10.8 746
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 PDB ENTRY 1PT3 2.5 37.05 7667 7446 794 97.1 0.241 0.241 0.2402 0.287 0.2882 RANDOM 38.4
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] -1.75 -1.75 3.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.19 c_mcangle_it 2.36 c_scbond_it 2.06 c_improper_angle_d 1.61 c_angle_deg 1.6 c_mcbond_it 1.4 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.19 c_mcangle_it 2.36 c_scbond_it 2.06 c_improper_angle_d 1.61 c_angle_deg 1.6 c_mcbond_it 1.4 c_bond_d 0.014 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 962 Nucleic Acid Atoms 486 Solvent Atoms 33 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing