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HUMAN NF-KAPPA-B P52 BOUND TO DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 THE PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE RESERVOIR SOLUTION CONTAINED 5% PEG 4000, 5 MM MGSO4, 50 MM MES PH 6.0 AND 3 MM DTT. DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR SOLUTION., vapor diffusion - hanging drop
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.2 α = 90 b = 121 β = 90 c = 134.9 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 120 IMAGE PLATE MARRESEARCH MIRRORS 1996-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.1 20 91.8 6.1 10.5 3.1 39642 39.9
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) 2.1 2.2 78.1 31.2 2.63 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 10 39039 3805 91.8 0.219 0.32 RANDOM 47.8
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] -5.7 8.4 -2.6
RMS Deviations Key Refinement Restraint Deviation x_scangle_it 6.85 x_mcangle_it 5.55 x_scbond_it 5.28 x_mcbond_it 3.87 x_angle_deg 2.1 x_improper_angle_d 1.64 x_bond_d 0.013 x_bond_d_na x_bond_d_prot x_angle_d
RMS Deviations Key Refinement Restraint Deviation x_scangle_it 6.85 x_mcangle_it 5.55 x_scbond_it 5.28 x_mcbond_it 3.87 x_angle_deg 2.1 x_improper_angle_d 1.64 x_bond_d 0.013 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4518 Nucleic Acid Atoms 445 Solvent Atoms 785 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing X-PLOR refinement DENZO data reduction SCALEPACK data scaling