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Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other yeast Sec13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 295 8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.78 74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.163 α = 90 b = 155.163 β = 90 c = 59.866 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 200 CCD ADSC QUANTUM 4 2006-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.3 40 92.6 0.092 0.084 11.9 2.7 21760 20444 -5 -5 63.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.3 3.42 76.3 0.418 0.347 2.1 2.2 1644
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT yeast Sec13 3.3 40 21760 18996 959 86.9 0.251 0.2416 0.305 0.2926 random 78.585
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] -10.926 -10.926 21.851
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 6.842 c_scangle_it 6.46 c_mcbond_it 4.025 c_scbond_it 3.972 c_angle_deg 1.636 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5168 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing RESOLVE phasing CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction