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AtVAL1 B3 domain in complex with 13bp-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% (w/v) PEG 5000 MME, 0.1M Tris base/Hydrochloric acid pH 8.0, 0.2M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.896 α = 90 b = 86.896 β = 90 c = 148.237 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2017-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
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 2.58 74.97 99.5 0.077 29.4 13.9 9191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.67
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 5YZY 2.58 30 7414 415 84.56 0.22757 0.22598 0.2296 0.25522 0.2533 RANDOM 44.338
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] -0.98 -0.98 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_4_deg 22.2 r_dihedral_angle_3_deg 19.037 r_dihedral_angle_1_deg 9.497 r_long_range_B_refined 8.865 r_long_range_B_other 8.865 r_mcangle_other 6.496 r_mcangle_it 6.491 r_scangle_other 6.459 r_scbond_it 3.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_4_deg 22.2 r_dihedral_angle_3_deg 19.037 r_dihedral_angle_1_deg 9.497 r_long_range_B_refined 8.865 r_long_range_B_other 8.865 r_mcangle_other 6.496 r_mcangle_it 6.491 r_scangle_other 6.459 r_scbond_it 3.972 r_scbond_other 3.953 r_mcbond_it 3.811 r_mcbond_other 3.783 r_angle_refined_deg 1.895 r_angle_other_deg 1.326 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 866 Nucleic Acid Atoms 527 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing