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Crystal structure of 2012 NSW GII.4 P domain in complex with Nano-85
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OOS PDB entry 4OOS was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7E for Nano-85 (molecule 2) experimental model PDB 4X7E PDB entry 4OOS was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7E for Nano-85 (molecule 2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 8000, HEPES
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.64 α = 90 b = 93.58 β = 90 c = 136.68 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 46.79 99.4 0.083 0.097 11.74 3.7 49811 -3 32.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 98.4 0.661 0.767 2.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4OOS was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7E for Nano-85 (molecule 2) 2.15 46.79 1.36 49738 2489 99.42 0.1975 0.1955 0.198 0.2379 0.239 39.688
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 f_dihedral_angle_d 13.713 f_angle_d 1.264 f_chiral_restr 0.057 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6340 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 8
Software Software Software Name Purpose XDS data reduction PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing