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Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R7Q PDB ENTRY 2R7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to equilibrate at 12 C by hanging-drop vapor diffusion with a well solution identical in composition to the drop except for the protein. With micro-seeding, thin, plate-like crystals appeared after 1 day and grew to full size in about two weeks., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76 α = 90 b = 143.766 β = 90.65 c = 112.833 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 100 CCD ADSC QUANTUM 315 Undulator A 2006-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C
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 2.8 30 81.9 0.051 17.8 2.8 49581
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) 2.8 2.9 62.2 0.339 2.4 3699
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 2R7Q 2.8 30 49581 3987 83.1 0.233 0.2172 0.277 0.2606 RANDOM 51.904
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 5.594 c_mcangle_it 3.673 c_scbond_it 3.635 c_mcbond_it 2.153
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17390 Nucleic Acid Atoms 290 Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement SHARP phasing DM phasing PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing