X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K35 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.7293100 mM Bis-Tris pH 5.7, 1.6 M (NH4)2SO4, and 10% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.6253.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.192α = 90
b = 91.192β = 90
c = 143.997γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.134899.60.190.99710.710.43793639.58
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.2598.21.760.7091.68.6

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 REPLACEMENTTHROUGHOUT3K352.1345.635984195199.570.16160.16070.179RANDOM38.214
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]
-19.22-19.2238.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.143
r_dihedral_angle_4_deg21.481
r_dihedral_angle_3_deg16.261
r_dihedral_angle_1_deg7.132
r_angle_refined_deg1.868
r_angle_other_deg1.422
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.143
r_dihedral_angle_4_deg21.481
r_dihedral_angle_3_deg16.261
r_dihedral_angle_1_deg7.132
r_angle_refined_deg1.868
r_angle_other_deg1.422
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4360
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction