X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KMG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72938% PEG 3350, 200 mM L-Proline, 100 mM Hepes pH 7.7
Crystal Properties
Matthews coefficientSolvent content
3.3262.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.806α = 90
b = 260.59β = 90
c = 94.997γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.723098.80.0510.99913.41397212
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)
11.721.8298.80.630.9733.413.4

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 REPLACEMENTTHROUGHOUT7KMG1.7229.3992421479198.520.19630.19390.2423RANDOM40.618
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]
-24.69-19.9644.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_sphericity_bonded32.816
r_sphericity_free14.656
r_dihedral_angle_3_deg13.768
r_dihedral_angle_4_deg12.889
r_dihedral_angle_1_deg7.073
r_rigid_bond_restr1.46
r_angle_refined_deg1.1
r_chiral_restr0.091
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_sphericity_bonded32.816
r_sphericity_free14.656
r_dihedral_angle_3_deg13.768
r_dihedral_angle_4_deg12.889
r_dihedral_angle_1_deg7.073
r_rigid_bond_restr1.46
r_angle_refined_deg1.1
r_chiral_restr0.091
r_gen_planes_refined0.005
r_bond_refined_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4622
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing