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Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G5N PDB ENTRY 5G5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 10 MM TRIS-HCL PH 8.5, 20% (W/V) PEG3350, 0.2 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.79 α = 90 b = 126.88 β = 106.15 c = 120.94 γ = 90
Symmetry Space Group P 1 21 1
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 TWO CYLINDRICAL PARABOLIC VERTICAL FOCUSSING MIRRORS 2013-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 30 94.3 0.2 3.8 3.3 130350
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 2.11 87.6 0.72 1.4 3.4
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 ENTRY 5G5N 2 30 128200 1945 94.17 0.17305 0.17224 0.1801 0.22569 0.2318 RANDOM 21.767
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] 0.39 -1.44 0.72 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.052 r_dihedral_angle_4_deg 15.454 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 6.882 r_scangle_it 2.15 r_mcangle_it 1.833 r_angle_refined_deg 1.45 r_scbond_it 1.296 r_mcbond_it 1.118 r_mcbond_other 1.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.052 r_dihedral_angle_4_deg 15.454 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 6.882 r_scangle_it 2.15 r_mcangle_it 1.833 r_angle_refined_deg 1.45 r_scbond_it 1.296 r_mcbond_it 1.118 r_mcbond_other 1.116 r_angle_other_deg 0.925 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.203 r_nbtor_refined 0.17 r_nbd_other 0.155 r_symmetry_vdw_other 0.151 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.083 r_nbtor_other 0.071 r_xyhbond_nbd_other 0.038 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other 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 15535 Nucleic Acid Atoms Solvent Atoms 1525 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing