6RNQ

Crystal structure of the dimerization domain of Gemin5 at 1.95 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15200 mM NaK Tartrate, 25% PEG 3350 and 100 mM BisTris Methane pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.2762.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.219α = 90
b = 54.972β = 104.3
c = 103.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9792ALBAXALOC

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
11.95100.499.170.999.963.45155841.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.02

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADFREE R-VALUE1.95100.41.3351194253999.170.21180.21060.235464.57
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_d18.144
f_angle_d0.8741
f_chiral_restr0.0451
f_bond_d0.0116
f_plane_restr0.0057
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3819
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
AutoSolphasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
PHENIXmodel building
Cootmodel building