X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529815% PEG 4000 0.1 M sodium acetate 0.4 M ammonium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
4.3772

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.61α = 90
b = 74.33β = 96.74
c = 62.31γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2016-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.246.419853.66356
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)
13.2960.51.53.5

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 REPLACEMENTTHROUGHOUT6EHD3.246.41620632359.260.213810.212270.24435RANDOM77.525
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]
-2.57-1.21-2.685.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.718
r_dihedral_angle_3_deg19.983
r_long_range_B_refined11.335
r_long_range_B_other11.333
r_dihedral_angle_1_deg8.927
r_dihedral_angle_4_deg7.914
r_mcangle_it7.654
r_mcangle_other7.651
r_scangle_other6.921
r_mcbond_other4.587
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.718
r_dihedral_angle_3_deg19.983
r_long_range_B_refined11.335
r_long_range_B_other11.333
r_dihedral_angle_1_deg8.927
r_dihedral_angle_4_deg7.914
r_mcangle_it7.654
r_mcangle_other7.651
r_scangle_other6.921
r_mcbond_other4.587
r_mcbond_it4.586
r_scbond_it4.106
r_scbond_other4.106
r_angle_refined_deg1.528
r_angle_other_deg0.93
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2467
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing