7XHR | pdb_00007xhr

Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GQM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES293cell-free crystallization
Crystal Properties
Matthews coefficientSolvent content
1.6324.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.61α = 90
b = 103.61β = 90
c = 103.61γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1SPring-8BL32XU

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.8501000.98995.539917297
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.810.53261.53

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5gqm1.80142.29917297174299.9880.1530.14950.160.1840.215.194
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_4_deg21.503
r_dihedral_angle_3_deg12.359
r_dihedral_angle_1_deg7.366
r_lrange_it3.389
r_lrange_other3.318
r_scangle_it2.511
r_scangle_other2.511
r_scbond_other1.635
r_scbond_it1.633
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2006
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrystFELdata scaling
Cootmodel building
XDSdata reduction
PHASERphasing