X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION296Mb(H64G,V68A) at 3.6 mM in 20 mM Tris-HCl pH 8.4, 1 mM EDTA, was mixed with an equal volume of reservoir solution (200 mM Tris-HCl pH 8.9 and 2.46 M ammonium sulfate). The crystal was dunked in a cryoprotection solution (reservoir buffer supplemented with 9% sucrose (w/v), 2% glucose (w/v), 8% glycerol (v/v), and 8% ethylene glycol (v/v)) prior to being flash-frozen in liquid nitrogen. Note that imidazole was present in lysis buffer at 10 mM prior to two-step purification.
Crystal Properties
Matthews coefficientSolvent content
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.425α = 90
b = 90.425β = 90
c = 45.442γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9791APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.0478.3199.60.0670.0220.99518.29.21014478.65
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.041.060.5040.2340.8172.7

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-VALUE6M8F1.0478.311.35101444508099.60.1290.12840.140615.27
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_d14.4027
f_angle_d1.0192
f_chiral_restr0.0781
f_bond_d0.0076
f_plane_restr0.0064
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1207
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms58

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing