X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DVQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277100mM potassium phosphate, 150mM NaCl, 4% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.18α = 90
b = 84.6β = 90
c = 85.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors2018-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.447.0297.60.0450.046129.3417.24910530130.218
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.48901.1341.1740.7632.1614.394

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 REPLACEMENTTHROUGHOUT4DVQ1.447.02100071523097.60.14090.13970.1634RANDOM28.886
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]
-0.240.58-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg17.24
r_dihedral_angle_3_deg12.911
r_dihedral_angle_1_deg5.989
r_rigid_bond_restr4.501
r_angle_refined_deg1.53
r_angle_other_deg1.405
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.198
r_dihedral_angle_4_deg17.24
r_dihedral_angle_3_deg12.911
r_dihedral_angle_1_deg5.989
r_rigid_bond_restr4.501
r_angle_refined_deg1.53
r_angle_other_deg1.405
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3812
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms130

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ARP/wARPdata reduction
PHASERphasing