X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZCD1zcd, 2yk1
experimental modelPDB 2YK11zcd, 2yk1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292100 mM Tris pH 8.5, 100 mM MgCl2, 100 mM NaCl, 32 % PEG400
Crystal Properties
Matthews coefficientSolvent content
4.266.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.788α = 90
b = 92.163β = 109.885
c = 139.105γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.979ESRFID30B

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
12.0424.8694.10.0870.9991613.19489352.71
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.3467.61.680.4281.811.1

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1zcd, 2yk12.0424.861.3594883241456.060.19910.19820.234778.38
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_d10.4573
f_angle_d0.6549
f_chiral_restr0.0449
f_plane_restr0.0045
f_bond_d0.0038
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11858
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms185

Software

Software
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building