4D1F

Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, first P212121 crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D0VPDB ENTRY 4D0V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510 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 coefficientSolvent content
1.831

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.66α = 90
b = 122.45β = 90
c = 133.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rTOROIDAL FOCUSING MIRROR2012-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.73099.70.1710.19.33648455.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8599.80.882.89

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4D0V2.729.8932882205799.540.214420.212270.24736THIN SHELLS49.454
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]
5.98-2.06-3.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.355
r_dihedral_angle_4_deg22.945
r_dihedral_angle_3_deg17.72
r_scangle_it6.68
r_dihedral_angle_1_deg6.311
r_scbond_it3.828
r_mcangle_it1.934
r_angle_refined_deg1.251
r_mcbond_it0.877
r_symmetry_vdw_refined0.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.355
r_dihedral_angle_4_deg22.945
r_dihedral_angle_3_deg17.72
r_scangle_it6.68
r_dihedral_angle_1_deg6.311
r_scbond_it3.828
r_mcangle_it1.934
r_angle_refined_deg1.251
r_mcbond_it0.877
r_symmetry_vdw_refined0.387
r_symmetry_hbond_refined0.318
r_nbtor_refined0.308
r_nbd_refined0.21
r_xyhbond_nbd_refined0.122
r_chiral_restr0.078
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms9574
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing