X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U4Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8293200 mM potassium acetate, 14-24% PEG3350, 2 mM NAD
Crystal Properties
Matthews coefficientSolvent content
2.5351.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 214.503α = 90
b = 78.529β = 91.01
c = 87.949γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.98SLSX06SA

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
12.245.61970.9916.94.269067
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)
12.22.250.92

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 REPLACEMENTTHROUGHOUT5U4Q2.245.6169067357697.690.18080.17840.2271RANDOM34.208
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]
-1.66-0.38-1.923.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_dihedral_angle_4_deg21.389
r_dihedral_angle_3_deg16.259
r_dihedral_angle_1_deg7.141
r_angle_refined_deg1.566
r_angle_other_deg1.319
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.656
r_dihedral_angle_4_deg21.389
r_dihedral_angle_3_deg16.259
r_dihedral_angle_1_deg7.141
r_angle_refined_deg1.566
r_angle_other_deg1.319
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9705
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing