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Crystal structure of Glycoprotein C from Puumala virus in the post-fusion conformation (pH 8.0)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 40% PEG 400
0.2 M Lithium sulphate
0.1 M Tris buffer pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.521 α = 90 b = 138.521 β = 90 c = 138.521 γ = 90
Symmetry Space Group I 21 3
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 PILATUS3 6M 2015-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.5 49 99.6 0.072 0.998 14.43 5.5 15391 -3 60.944
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 2.5 2.53 99.6 0.783 2.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 5J81 2.5 49 14611 780 99.55 0.211 0.2085 0.2169 0.2579 0.2144 RANDOM 67.716
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 r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_4_deg 10.663 r_dihedral_angle_1_deg 7.386 r_mcangle_it 1.492 r_angle_refined_deg 1.271 r_angle_other_deg 0.856 r_mcbond_it 0.83 r_mcbond_other 0.83 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.944 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_4_deg 10.663 r_dihedral_angle_1_deg 7.386 r_mcangle_it 1.492 r_angle_refined_deg 1.271 r_angle_other_deg 0.856 r_mcbond_it 0.83 r_mcbond_other 0.83 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3149 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing