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Crystal structure of the human Adenovirus type 21 fiber knob
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H7Z PDB ENTRY 1H7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 298 22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85 α = 90 b = 63.92 β = 91.7 c = 209.35 γ = 90
Symmetry Space Group P 1 2 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 PIXEL PSI PILATUS 6M 2007-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.5 49.45 91.6 0.11 8.83 3 78468 71876 -3
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) 2.5 2.68 78.8 0.203 4.2 2.1
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 1H7Z 2.5 49.45 68282 3593 91.62 0.23543 0.23418 0.2337 0.25905 0.2569 RANDOM 20.222
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] -0.21 -0.36 -0.99 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.455 r_dihedral_angle_4_deg 19.034 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.03 r_scangle_it 4.259 r_mcangle_it 3.916 r_scbond_it 2.818 r_mcbond_it 2.374 r_angle_refined_deg 0.594 r_symmetry_vdw_refined 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.455 r_dihedral_angle_4_deg 19.034 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.03 r_scangle_it 4.259 r_mcangle_it 3.916 r_scbond_it 2.818 r_mcbond_it 2.374 r_angle_refined_deg 0.594 r_symmetry_vdw_refined 0.346 r_nbtor_refined 0.328 r_symmetry_hbond_refined 0.327 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17035 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction XSCALE data scaling PHASER phasing