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Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OUP PDB ENTRY 1OUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% PEG3350, 0.2 M DI-SODIUM TARTRATE DEHYDRATE, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.45 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.636 α = 74.45 b = 64.705 β = 73.56 c = 79.157 γ = 75.56
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 CCD ADSC CCD MIRRORS 2005-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 2.9 37.09 97.2 0.08 17.5 3.6 24597 83.5
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 2.9 3 97.2 0.3 3.3 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OUP 2.9 37.09 24597 1922 95.4 0.237 0.237 0.2294 0.284 0.277 RANDOM 61
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] -5.52 -14.52 -10.35 -4.06 -17.18 9.58
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 7.63 c_mcangle_it 6.24 c_scbond_it 5.67 c_mcbond_it 4.19 c_angle_deg 1.5 c_improper_angle_d 1.27 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 7.63 c_mcangle_it 6.24 c_scbond_it 5.67 c_mcbond_it 4.19 c_angle_deg 1.5 c_improper_angle_d 1.27 c_bond_d 0.009 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 6902 Nucleic Acid Atoms 1868 Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing