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Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, F23 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D0V PDB ENTRY 4D0V CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10 MM TRIS-HCL, 1.7 M AMMONIUM SULFATE, 0.085 M HEPES SODIUM SALT PH 7.5, 1.7%(V/V) POLYETHYLENE GLYCOL (PEG) 400, 15%(V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 1.7 27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.52 α = 90 b = 121.52 β = 90 c = 121.52 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 KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING 2013-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.33 43 99.5 0.05 18.5 5.8 33985 15.6
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 1.33 1.36 95.3 0.37 2.2 2.4
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 4D0V CHAIN A 1.33 42.96 32152 1832 99.53 0.11848 0.11733 0.1248 0.13804 0.1398 RANDOM 21.225
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] -1.74 2.47 -5.69 -2.73 -2.36 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 25.548 r_dihedral_angle_2_deg 25.168 r_dihedral_angle_3_deg 12.22 r_sphericity_bonded 11.235 r_dihedral_angle_1_deg 6.485 r_rigid_bond_restr 5.279 r_scangle_it 3.865 r_scbond_it 3.427 r_mcangle_it 2.356 r_mcbond_other 1.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 25.548 r_dihedral_angle_2_deg 25.168 r_dihedral_angle_3_deg 12.22 r_sphericity_bonded 11.235 r_dihedral_angle_1_deg 6.485 r_rigid_bond_restr 5.279 r_scangle_it 3.865 r_scbond_it 3.427 r_mcangle_it 2.356 r_mcbond_other 1.887 r_mcbond_it 1.864 r_angle_refined_deg 1.614 r_angle_other_deg 0.813 r_symmetry_hbond_refined 0.357 r_symmetry_vdw_refined 0.347 r_nbd_refined 0.252 r_symmetry_hbond_other 0.209 r_nbd_other 0.192 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_other 0.163 r_chiral_restr 0.116 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.037 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 859 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing