X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F9V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5289.1530% PEG 500 MME/PEG 20000, 0.1 M Tris/Bicine pH 8.5 and 60 mM divalent cations [Molecular Dimensions (Rotherham, UK) Morpheus A9]
Crystal Properties
Matthews coefficientSolvent content
3.0659.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.229α = 84.95
b = 103.395β = 85.493
c = 115.416γ = 81.549
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9282DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.6114.7197.20.0610.9986.46.9432760
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.630.8590.344

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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.679.4524327352161697.1420.1820.18080.210924.203
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]
-0.631-0.106-0.2070.338-0.0670.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.383
r_dihedral_angle_3_deg14.876
r_dihedral_angle_2_deg8.217
r_lrange_it6.406
r_dihedral_angle_1_deg6.217
r_scangle_it4.292
r_scbond_it2.934
r_mcangle_it2.137
r_angle_refined_deg1.939
r_mcbond_it1.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.383
r_dihedral_angle_3_deg14.876
r_dihedral_angle_2_deg8.217
r_lrange_it6.406
r_dihedral_angle_1_deg6.217
r_scangle_it4.292
r_scbond_it2.934
r_mcangle_it2.137
r_angle_refined_deg1.939
r_mcbond_it1.453
r_nbtor_refined0.309
r_symmetry_nbd_refined0.268
r_nbd_refined0.235
r_xyhbond_nbd_refined0.209
r_symmetry_xyhbond_nbd_refined0.171
r_chiral_restr0.134
r_metal_ion_refined0.089
r_bond_refined_d0.015
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19974
Nucleic Acid Atoms
Solvent Atoms2329
Heterogen Atoms800

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing