2WB6 | pdb_00002wb6

Crystal structure of AFV1-102, a protein from the Acidianus Filamentous Virus 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.5-2M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 2% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.89α = 90
b = 62.89β = 90
c = 110.837γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.9554.4799.50.114.434.7100062
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)
11.9521000.590.838

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.9554.47947248199.240.216190.213390.21690.274310.2782RANDOM38.031
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]
-0.6-0.3-0.60.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.554
r_dihedral_angle_3_deg13.617
r_rigid_bond_restr12.305
r_scbond_it10.81
r_scangle_it8.131
r_dihedral_angle_4_deg7.775
r_dihedral_angle_1_deg5.982
r_sphericity_bonded5.484
r_sphericity_free3.987
r_mcangle_it2.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.554
r_dihedral_angle_3_deg13.617
r_rigid_bond_restr12.305
r_scbond_it10.81
r_scangle_it8.131
r_dihedral_angle_4_deg7.775
r_dihedral_angle_1_deg5.982
r_sphericity_bonded5.484
r_sphericity_free3.987
r_mcangle_it2.473
r_angle_refined_deg1.313
r_mcbond_it1.279
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms906
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing