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Early B-cell Factor 1 (Ebf1) bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 310 10% PEG4000, 10% isopropanol, 100mM sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.49 α = 88.99 b = 78.69 β = 90 c = 103.57 γ = 77.81
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 MAR CCD 165 mm 2006-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9537 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 96.7 0.089 9.9 2.3 53552 52163 2 49.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 3 96.2 0.46 2.3 2.2
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 3MLN 2.8 38.75 52163 49243 2592 100 0.20661 0.20355 0.2038 0.26411 0.2621 RANDOM 50.366
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] 4.02 -1.21 -0.63 -0.05 0.95 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.449 r_dihedral_angle_1_deg 7.176 r_scangle_it 2.326 r_scbond_it 1.636 r_mcangle_it 1.464 r_angle_refined_deg 1.411 r_mcbond_it 0.876 r_angle_other_deg 0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.449 r_dihedral_angle_1_deg 7.176 r_scangle_it 2.326 r_scbond_it 1.636 r_mcangle_it 1.464 r_angle_refined_deg 1.411 r_mcbond_it 0.876 r_angle_other_deg 0.858 r_mcbond_other 0.241 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9950 Nucleic Acid Atoms 1792 Solvent Atoms 150 Heterogen Atoms 69
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling