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Structure of the DNA-binding domain of SEPALLATA 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 potassium sodium tartrate tetrahydrate (0.2M), bis-tris propane (0.1M, pH 7.5) and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.404 α = 90 b = 67.436 β = 90 c = 122.568 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 PIXEL DECTRIS PILATUS 6M-F 2017-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.1 48 99 0.077 0.084 0.998 15.2 6 16555 52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 95.6 1.25 1.3 0.564 1.39 4.1
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 3KOV 2.1 47.72 14874 1651 98.97 0.20683 0.20351 0.2103 0.23592 0.2394 RANDOM 55.465
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] -0.8 0.42 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 22.578 r_dihedral_angle_3_deg 15.263 r_long_range_B_refined 7.003 r_long_range_B_other 6.95 r_dihedral_angle_1_deg 5.661 r_scangle_other 4.777 r_mcangle_it 3.716 r_mcangle_other 3.715 r_scbond_it 3.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 22.578 r_dihedral_angle_3_deg 15.263 r_long_range_B_refined 7.003 r_long_range_B_other 6.95 r_dihedral_angle_1_deg 5.661 r_scangle_other 4.777 r_mcangle_it 3.716 r_mcangle_other 3.715 r_scbond_it 3.093 r_scbond_other 3.093 r_mcbond_it 2.537 r_mcbond_other 2.52 r_angle_refined_deg 1.237 r_angle_other_deg 1.048 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1814 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing