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Structure of Ndt80 (Residues 59-340) DNA-binding domain core
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 4000, sodium acetate, magnesium chloride, spermine, 20mer DNA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.91 35.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.88 α = 90 b = 41.93 β = 90 c = 164.5 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 4 bent cylindrical Si-mirror (Rh coating) 2002-05-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9563 APS 14-BM-D
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 2.2 14.95 98.1 0.076 20.9 11.7 12530 13292 -3 14.3
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) 2.2 2.25 100 0.221 7.9 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.2 14.95 13291 13086 626 98.5 0.229 0.229 0.226 0.2252 0.268 0.27 random
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] 5.73 -1.32 -4.41
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.524 c_scbond_it 3.177 c_mcangle_it 2.29 c_mcbond_it 1.837 c_angle_deg 1.3 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1989 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing CNS refinement