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Crystal structure of the human Adenovirus type 7 fiber knob
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EXV Human Adenovirus type 11 fiber knob
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293.15 23% w/v PEG 3350, 0.1M HEPES buffer, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.31 α = 90 b = 88.05 β = 90 c = 79.17 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 93.15 CCD MARMOSAIC 225 mm CCD 2006-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 79.06 99.1 0.05 5.1 59433 52966 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 95.1 0.364 1.34 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Human Adenovirus type 11 fiber knob 1.75 36.11 59433 52966 5916 99.08 0.19572 0.19192 0.1976 0.22999 0.2343 RANDOM 16.948
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] -1.2 -1.03 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_1_deg 18.09 r_dihedral_angle_3_deg 12.441 r_scangle_it 2.365 r_scbond_it 1.695 r_mcangle_it 1.144 r_mcbond_it 0.983 r_angle_refined_deg 0.732 r_angle_other_deg 0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.472 r_dihedral_angle_4_deg 19.272 r_dihedral_angle_1_deg 18.09 r_dihedral_angle_3_deg 12.441 r_scangle_it 2.365 r_scbond_it 1.695 r_mcangle_it 1.144 r_mcbond_it 0.983 r_angle_refined_deg 0.732 r_angle_other_deg 0.651 r_symmetry_vdw_other 0.285 r_symmetry_vdw_refined 0.271 r_nbd_other 0.218 r_nbd_refined 0.212 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.178 r_mcbond_other 0.173 r_symmetry_hbond_refined 0.17 r_nbtor_other 0.084 r_chiral_restr 0.054 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4636 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling