X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KNP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527710% w/v PEG 8000, 20% v/v ethylene glycol, 0.075 %(w/v) of each Additive, 5 %(v/v) EtOH, 0.1 M MOPS/HEPES-Na, pH 7.5, Additive: 0.75 %(w/v) menthol, 0.75 %(w/v) caffeic acid, 0.75 %(w/v) D-quinic acid, 0.75 %(w/v) shikimic acid, 0.75 %(w/v) gallic acid monohydrate, 0.75 %(w/v) N-vanillylnonanamide.
Crystal Properties
Matthews coefficientSolvent content
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.399α = 93.89
b = 52.31β = 101.92
c = 73.089γ = 106.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97950ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.3538.2787.90.0620.0790.0490.9898.72.480704
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4281.30.4380.5590.3450.7482.12.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1KNP1.3538.2660.9180678724780.730.17430.17280.2026
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d2.008
f_angle_d0.756
f_chiral_restr0.057
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2784
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing