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Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FP8 PDB 4FP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M sodium citrate pH 5.5 and 9% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.344 α = 90 b = 88.344 β = 90 c = 255.038 γ = 90
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 2016-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim 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 1.97 88.4 99.5 0.155 0.066 15.4 6.3 136341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 99.5 0.82 0.353 0.722 2 6.2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 4FP8 1.97 88.34 129540 6721 99.46 0.18254 0.18124 0.189 0.2083 0.2149 RANDOM 34.142
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] -0.09 -0.09 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 16.344 r_dihedral_angle_3_deg 14.181 r_long_range_B_refined 7.449 r_long_range_B_other 7.449 r_dihedral_angle_1_deg 7.058 r_scangle_other 2.04 r_mcangle_it 2 r_mcangle_other 2 r_angle_refined_deg 1.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 16.344 r_dihedral_angle_3_deg 14.181 r_long_range_B_refined 7.449 r_long_range_B_other 7.449 r_dihedral_angle_1_deg 7.058 r_scangle_other 2.04 r_mcangle_it 2 r_mcangle_other 2 r_angle_refined_deg 1.599 r_scbond_it 1.217 r_scbond_other 1.188 r_mcbond_it 1.115 r_mcbond_other 1.112 r_angle_other_deg 0.966 r_chiral_restr 0.1 r_bond_refined_d 0.013 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 10771 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement PHASER phasing HKL-2000 data scaling HKL-2000 data reduction