X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
2.1141.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.42α = 90
b = 49.42β = 90
c = 267.12γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9201NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.5142.899.790.1920.9971011.81253150.77
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)
12.512.60.512

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4DBG2.5142.81.391252860699.80.21420.21140.2701RANDOM61.82
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
f_dihedral_angle_d3.5865
f_angle_d0.5487
f_chiral_restr0.0333
f_plane_restr0.0038
f_bond_d0.0019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2990
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms30

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
Cootmodel building
XDSdata reduction