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Rift valley fever virus Gn in complex with a neutralizing antibody fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% w/v PEG 500, 0.1 M bis-Tris pH 6.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.59 α = 81.01 b = 61.95 β = 77.52 c = 78.91 γ = 84.74
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 2017-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.98 23.6 96.2 0.072 0.98 5.8 1.8 59882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 95.3 0.651 0.67 1.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4J02 1.98 23.6 59882 3141 96.24 0.20478 0.20264 0.24343 0.2612 RANDOM 46.972
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] -2.4 -0.77 0.97 1.74 0.28 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.078 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.719 r_long_range_B_refined 5.027 r_long_range_B_other 4.926 r_mcangle_it 2.485 r_mcangle_other 2.485 r_scangle_other 2.26 r_mcbond_it 1.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.078 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.719 r_long_range_B_refined 5.027 r_long_range_B_other 4.926 r_mcangle_it 2.485 r_mcangle_other 2.485 r_scangle_other 2.26 r_mcbond_it 1.471 r_mcbond_other 1.471 r_angle_refined_deg 1.422 r_scbond_it 1.399 r_scbond_other 1.395 r_angle_other_deg 0.897 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7049 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing