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DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 10% PEG-4000, 200mM KCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.2 α = 90 b = 100.7 β = 101.2 c = 72 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 MARMOSAIC 225 mm CCD 2009-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 2.4 29.31 99.6 0.083 14.8 4.6 39094 38953 2 39
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 2.4 2.5 98 0.459 3.2 4.4 4454
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 3MLO 2.4 29.31 39094 37005 1948 100 0.17338 0.17096 0.1851 0.21861 0.2284 RANDOM 51.571
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] 1.39 0.31 0.48 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.906 r_dihedral_angle_4_deg 18.376 r_dihedral_angle_3_deg 15.008 r_dihedral_angle_1_deg 6.522 r_scangle_it 2.352 r_scbond_it 1.569 r_angle_refined_deg 1.35 r_mcangle_it 1.045 r_mcbond_it 0.548 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.906 r_dihedral_angle_4_deg 18.376 r_dihedral_angle_3_deg 15.008 r_dihedral_angle_1_deg 6.522 r_scangle_it 2.352 r_scbond_it 1.569 r_angle_refined_deg 1.35 r_mcangle_it 1.045 r_mcbond_it 0.548 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4664 Nucleic Acid Atoms 896 Solvent Atoms 445 Heterogen Atoms 2
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling