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Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKX PDB entry 1VKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 289 50mM BTP pH 6.3, 50mM CaCl2, 7% w/v PEG 3000, 1mM Spermine, 10mM DTT, 8% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.1 69.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.493 α = 90 b = 167.493 β = 90 c = 172.757 γ = 90
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 ADSC QUANTUM 210 2003-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0688 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.5 50 99.6 0.076 23.101 7.2 47283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.5 3.64 96.5 0.848 5.5 4576
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1VKX 3.59 46.45 6020 45190 4541 81.2 0.245 0.2593 0.301 0.313 150.501
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] -2.977 -2.977 5.954
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 16.599 c_mcangle_it 12.762 c_scbond_it 11.977 c_mcbond_it 8.061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18520 Nucleic Acid Atoms 2120 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction ADSC data collection PHASER phasing