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2.0 Angstrom Structure of the Ile74Val Variant of Vivid (VVD).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Protein at 3.6 mg/ml dissolved in Buffer containing 5 mM DTT, 100 mM NaCl, 50 mM HEPES pH 8.0 and 10% glycerol is combined with an equal volume of 28% PEG 4k, 100 mM ammonium acetate, 100 mM trisodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.78 α = 90 b = 80.3 β = 94.76 c = 56.9 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 80 CCD ADSC QUANTUM 210 2008-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.979 CHESS F2
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 2 35.66 99.2 0.076 29 21712 21712 4.5
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) 2 2.07 93.9 0.349 4.5 1903
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 MOLECULAR REPLACEMENT 2pd7 2 30 21712 21549 2117 99.2 0.261 0.261 0.244 0.2458 0.261 0.2644 Random 33.546
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] -3.492 7.137 10.768 -7.276
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.731 c_mcangle_it 2.004 c_scbond_it 1.809 c_mcbond_it 1.212
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 106
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling