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Crystal structure of a putative transposase (dr_0177) from deinococcus radiodurans r1 at 1.90 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F4F 2f4f chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.27 62.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.787 α = 90 b = 66.787 β = 90 c = 81.18 γ = 120
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 ADSC QUANTUM 4 2004-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 28.915 100 0.045 0.045 9.9 3.9 31895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.547 0.547 1.3 2.9
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 (All) 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 2f4f chain A 1.9 27.24 31862 1608 99.87 0.162 0.16159 0.16 0.169 0.191 0.1958 RANDOM 40.291
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] 0.43 0.21 0.43 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 20.437 r_dihedral_angle_3_deg 13.763 r_scangle_it 7.198 r_dihedral_angle_1_deg 6.243 r_scbond_it 5.748 r_mcangle_it 3.378 r_mcbond_it 2.466 r_angle_refined_deg 1.703 r_angle_other_deg 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 20.437 r_dihedral_angle_3_deg 13.763 r_scangle_it 7.198 r_dihedral_angle_1_deg 6.243 r_scbond_it 5.748 r_mcangle_it 3.378 r_mcbond_it 2.466 r_angle_refined_deg 1.703 r_angle_other_deg 0.87 r_mcbond_other 0.609 r_symmetry_vdw_other 0.273 r_nbd_refined 0.21 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.184 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.113 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.018 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing