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Crystal structure of raptor adenovirus 1 fibre head, wild-type form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZPE PDB ENTRY 3ZPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 20 MM BICINE-NAOH PH 9.0, 50 MM MAGNESIUM CHLORIDE, 5 MM L-ARGININE, 5% (V/V) GLYCEROL, 1.5 M SODIUM CHLORIDE, 10% (V/V) ETHANOL
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.72 α = 90 b = 81.72 β = 90 c = 81.72 γ = 90
Symmetry Space Group P 21 3
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 VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 1.47 47.2 100 0.04 29.6 9.9 31365 17.7
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 1.47 1.49 100 0.6 3.2 8.8
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 3ZPE 1.47 45 29748 1586 99.98 0.1579 0.15682 0.1669 0.17862 0.1827 RANDOM 24.629
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.812 r_dihedral_angle_4_deg 24.864 r_dihedral_angle_3_deg 10.229 r_dihedral_angle_1_deg 7.121 r_scangle_it 4.312 r_scbond_it 2.789 r_mcangle_it 2.479 r_angle_refined_deg 1.661 r_mcbond_it 1.611 r_mcbond_other 1.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.812 r_dihedral_angle_4_deg 24.864 r_dihedral_angle_3_deg 10.229 r_dihedral_angle_1_deg 7.121 r_scangle_it 4.312 r_scbond_it 2.789 r_mcangle_it 2.479 r_angle_refined_deg 1.661 r_mcbond_it 1.611 r_mcbond_other 1.584 r_angle_other_deg 0.928 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.204 r_symmetry_vdw_other 0.171 r_nbtor_refined 0.17 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.104 r_nbtor_other 0.073 r_symmetry_hbond_refined 0.068 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 1069 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing