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Crystal structure of yeast proteasome interacting protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VLD PDB ENTRY 3VLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 1M sodium chloride, 0.5% PEG 3350, 0.8M lithium sulfate, 0.1M N-(2-acetamido) iminodiacetic acid, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 7.01 82.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.282 α = 90 b = 187.282 β = 90 c = 379.574 γ = 120
Symmetry Space Group P 65 2 2
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 RAYONIX MX225HE 2011-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 3.8 50 100 0.084 12.1 10.6 39787 -3
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) 1 3.8 3.87 99.9 0.527 7.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB ENTRY 3VLD 3.8 30 39285 1952 0.2505 0.2505 0.2514 0.2782 0.2773 RANDOM 163.3521
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]
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 17.554 c_mcangle_it 13.54 c_scbond_it 12.083 c_mcbond_it 8.733 c_angle_deg 0.81161 c_bond_d 0.006402
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8594 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MLPHARE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling