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2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from Influenza A virus (A/Puerto Rico/8/34(H1N1))
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 Protein: 12.8 mg/mL 10 mM Tris-HCl pH 8.3 500 mM NaCl 0.5 mM TCEP
Crsytallization: The JCSG+ Suite (B9: 100 mM Citric acid pH 4.0 20% (w/v) PEG 6000; final pH 5.0
Cryocondition: Crystallization condition + sucrose (50%)
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.367 α = 90 b = 117.896 β = 90 c = 40.256 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 300 mm CCD 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.1 30 99.9 0.074 25.6 7.2 22646 22646 37.8
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 2.1 2.14 100 0.599 3.5 6.5
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 1EA3 2.1 29.47 21413 1086 99.88 0.17603 0.17491 0.19745 0.2242 RANDOM 47.391
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] 4.36 -3.18 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.686 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_4_deg 8.588 r_dihedral_angle_1_deg 3.003 r_angle_refined_deg 1.497 r_angle_other_deg 1.054 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.686 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_4_deg 8.588 r_dihedral_angle_1_deg 3.003 r_angle_refined_deg 1.497 r_angle_other_deg 1.054 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 2451 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection PHASER phasing HKL-2000 data reduction Coot model building ARP model building HKL-2000 data scaling