X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8293100 mM TRIS/HCl, 1.25 M LiBr, 29% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1542.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 119.95β = 90
c = 66.58γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.73098.90.04417.75.232215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.899.10.5082.8

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 REPLACEMENTTHROUGHOUT5DAP1.73030596161098.890.1590.15730.1919RANDOM32.478
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]
-2.093.63-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.926
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg12.826
r_dihedral_angle_1_deg6.968
r_angle_refined_deg1.257
r_angle_other_deg1.155
r_rigid_bond_restr0.475
r_chiral_restr0.049
r_gen_planes_other0.007
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.926
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg12.826
r_dihedral_angle_1_deg6.968
r_angle_refined_deg1.257
r_angle_other_deg1.155
r_rigid_bond_restr0.475
r_chiral_restr0.049
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_refined_d0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2218
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing