X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.15XChem 0.045uls compound (0.5M) in DMSO echo dispensed into crystal drop Drop = 0.3uls protein + 0.3us well +0.001uls seeds. Protein = 25uls 30mgs/ml human PIF1 (206-620) in 10mM Tris pH 7.5, 175mM NaCl, 2%glycerol, 5mM DTT, 0.1mM PMSF + 21uls 10mM Tris, 2.7uls 0.2M MgCl2, 5uls 100mM AMPPNP + 27uls H2O. Well = 4% Glycerol, 27% PEG 2KMME, 0.1M NaAcetate, 0.1M Tris pH8.5. Set up on douglas instruments robot - tray on ice - set-up room temperature - crystallised 4 degrees C.
Crystal Properties
Matthews coefficientSolvent content
2.2445.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.6α = 90
b = 143.714β = 90
c = 77.238γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.72727.8399.60.99919.56.543220
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.770.866

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.72727.8343195213499.6170.1750.17340.211430.663
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]
-2.2080.9031.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.622
r_dihedral_angle_3_deg13.335
r_dihedral_angle_2_deg9.591
r_lrange_it7.677
r_scangle_it6.015
r_dihedral_angle_1_deg5.641
r_scbond_it4.131
r_mcangle_it3.331
r_mcbond_it2.479
r_angle_refined_deg1.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.622
r_dihedral_angle_3_deg13.335
r_dihedral_angle_2_deg9.591
r_lrange_it7.677
r_scangle_it6.015
r_dihedral_angle_1_deg5.641
r_scbond_it4.131
r_mcangle_it3.331
r_mcbond_it2.479
r_angle_refined_deg1.896
r_nbtor_refined0.309
r_nbd_refined0.23
r_xyhbond_nbd_refined0.189
r_symmetry_nbd_refined0.165
r_symmetry_xyhbond_nbd_refined0.14
r_chiral_restr0.122
r_bond_refined_d0.009
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3150
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing