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Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4D PDB entry 1p4d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 protein buffer: 50 mM NaCl, 10% glycerol, 10 mM Tris-HCl pH 7.5, mother liquor: 75 mM sodium nitrate, 14% w/v PEG 3350, 10 mM spermine, 110 uM oriT DNA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 35.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.888 α = 90 b = 88.259 β = 90 c = 127.293 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD monochromator 2005-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97173 APS 22-ID
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 2.42 50 97.9 0.098 9.6 5.1 20078 19657 29.5
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) 2.42 2.46 99.3 0.382 5.2
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 1p4d 2.42 44.13 20078 19657 1007 98.3 0.211 0.211 0.2108 0.27 0.27 RANDOM 44
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] -5.49 14.02 -8.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.72 c_mcangle_it 2.72 c_scbond_it 2.44 c_mcbond_it 1.61 c_angle_deg 1.2 c_improper_angle_d 0.75 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.72 c_mcangle_it 2.72 c_scbond_it 2.44 c_mcbond_it 1.61 c_angle_deg 1.2 c_improper_angle_d 0.75 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 4142 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing