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Crystal structure of the nucleocapsid protein from Schmallenberg virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other SBV NUCLEOCAPSID PROTEIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 CRYSTALLISATION CONDITION: 17% PEG10000, 100 MM BIS-TRIS PH 5.5, 100 MM AMMONIUM ACETATE. CRYO CONDITION: 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.31 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.03 α = 90 b = 81.03 β = 90 c = 128.551 γ = 120
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 315r MIRORS 2012-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 3.2 61.59 99.8 0.08 8.7 3.2 24459
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 2.75 2.9 100 0.56 2 3.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SBV NUCLEOCAPSID PROTEIN 2.75 61.59 23228 1219 99.72 0.16601 0.16411 0.164 0.20129 RANDOM 78.448
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] -8.9 -8.9 17.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_3_deg 15.083 r_dihedral_angle_4_deg 13.431 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.291 r_angle_other_deg 0.951 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.374 r_dihedral_angle_3_deg 15.083 r_dihedral_angle_4_deg 13.431 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.291 r_angle_other_deg 0.951 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7158 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing