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The structure of Pyrococcus Furiosus SfsA in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 290 3.8mM CaCl2 in 6% (w/v) PEG 6000, 0.2 M citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.7 α = 90 b = 42.69 β = 104.92 c = 88.9 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2009-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97957200 Diamond I02
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 2.2 43 99 0.09 3.4 29894 29894
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 2.2 2.32 98.7 0.4 3.4
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 4DA2 2.2 39.07 29894 28390 1493 98.86 0.24248 0.23963 0.239 0.29788 0.2973 RANDOM 37.927
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] 0.27 -0.25 -0.77 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 14.274 r_dihedral_angle_1_deg 6.065 r_scangle_it 2.491 r_scbond_it 1.484 r_mcangle_it 1.305 r_angle_refined_deg 1.231 r_angle_other_deg 0.805 r_mcbond_it 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 14.274 r_dihedral_angle_1_deg 6.065 r_scangle_it 2.491 r_scbond_it 1.484 r_mcangle_it 1.305 r_angle_refined_deg 1.231 r_angle_other_deg 0.805 r_mcbond_it 0.7 r_mcbond_other 0.099 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3676 Nucleic Acid Atoms 474 Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling