X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SBN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.2 M ammonium sulphate, 0.1 M sodium citrate pH 3.5, 28 % (v/v) PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.526α = 90
b = 98.268β = 90
c = 121.233γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.950500PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.357799.10.04314.984.05122029
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.420.439

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 REPLACEMENTTHROUGHOUT6SBN1.3576.34116011601199.110.11460.11270.1517RANDOM21.684
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]
-0.130.38-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.352
r_dihedral_angle_2_deg29.813
r_dihedral_angle_4_deg15.41
r_sphericity_bonded15.367
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg6.725
r_rigid_bond_restr5.799
r_angle_refined_deg2.43
r_angle_other_deg1.336
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.352
r_dihedral_angle_2_deg29.813
r_dihedral_angle_4_deg15.41
r_sphericity_bonded15.367
r_dihedral_angle_3_deg11.22
r_dihedral_angle_1_deg6.725
r_rigid_bond_restr5.799
r_angle_refined_deg2.43
r_angle_other_deg1.336
r_chiral_restr0.149
r_bond_refined_d0.026
r_gen_planes_refined0.015
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3995
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing