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Crystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp duplex DNA
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 4.8 HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1 MICRO L COMPLEX SOLUTION AND 1 MICRO L RESERVOIR SOLUTION CONSISTING OF 40 % MPD, 0.4 M AMMONIUM FORMATE AND 0.1 M ACETATE BUFFER (PH4.8) AT ROOM TEMPERATURE., pH 4.80
Crystal Properties Matthews coefficient Solvent content 3.53 64.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.8 α = 90 b = 106.8 β = 90 c = 60.2 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 113 CCD ADSC CCD MIRRORS 2004-12-14 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 2.8 50 99.6 0.08 31.7 10.74 9047 36.2
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 2.8 2.9 99.9 0.36 6.05 11.1
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 1PT3 2.8 47.76 8744 919 97.1 0.193 0.193 0.1941 0.265 0.2645 RANDOM 45.1
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] -4.91 -4.91 9.82
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.8 c_scangle_it 11.11 c_scbond_it 8.17 c_mcangle_it 7.52 c_mcbond_it 5.37 c_improper_angle_d 1.17 c_angle_deg 1 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.8 c_scangle_it 11.11 c_scbond_it 8.17 c_mcangle_it 7.52 c_mcbond_it 5.37 c_improper_angle_d 1.17 c_angle_deg 1 c_bond_d 0.006 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 1006 Nucleic Acid Atoms 732 Solvent Atoms 87 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling EPMR phasing