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Structure of the SCL:E47 complex bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPA PDB ENTRY 2YPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE
Crystal Properties Matthews coefficient Solvent content 2.8 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.193 α = 90 b = 152.882 β = 90 c = 55.412 γ = 90
Symmetry Space Group C 2 2 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 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 2.9 3 97.8 0.08 15.6 3.8 7203 1.2
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 2.9 3 98.5 0.97 1.5 3.7
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 2YPA 2.87 42.44 6860 331 96.93 0.25531 0.25381 0.2492 0.28828 0.286 RANDOM 117.195
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] 8.14 -3.96 -4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.275 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_4_deg 12.082 r_scangle_it 7.857 r_scbond_it 5.226 r_mcangle_it 5.215 r_dihedral_angle_1_deg 4.145 r_mcbond_it 3.057 r_angle_refined_deg 0.804 r_chiral_restr 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.275 r_dihedral_angle_3_deg 14.846 r_dihedral_angle_4_deg 12.082 r_scangle_it 7.857 r_scbond_it 5.226 r_mcangle_it 5.215 r_dihedral_angle_1_deg 4.145 r_mcbond_it 3.057 r_angle_refined_deg 0.804 r_chiral_restr 0.042 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1174 Nucleic Acid Atoms 448 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing