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Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, second P212121 crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D0V PDB ENTRY 4D0V
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) PEG 400, 15%(V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 1.8 31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.77 α = 90 b = 96.75 β = 90 c = 153.29 γ = 90
Symmetry Space Group P 21 21 21
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 CYLINDRICAL GRAZING INCIDENCE MIRROR BENT TO APPROXIMATE TO A TOROIDAL CURVATURE 2012-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.9 70 99.9 0.07 19.6 11.9 113650 25.1
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 1.9 2 99.9 0.39 6.5 12.1
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 4D0V 1.9 29.73 111478 2003 99.85 0.17437 0.17314 0.1745 0.23945 0.2399 THIN SHELLS 32.1
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] 0.04 0.69 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 14.923 r_scangle_it 9.324 r_dihedral_angle_1_deg 6.217 r_scbond_it 5.442 r_mcangle_it 2.609 r_angle_refined_deg 1.385 r_mcbond_it 1.317 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 14.923 r_scangle_it 9.324 r_dihedral_angle_1_deg 6.217 r_scbond_it 5.442 r_mcangle_it 2.609 r_angle_refined_deg 1.385 r_mcbond_it 1.317 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_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 9718 Nucleic Acid Atoms Solvent Atoms 887 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing