X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EN5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M MES pH6.5, 0.21 M NaCl, 11.5% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7755.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.557α = 90
b = 145.409β = 90
c = 175.612γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97625PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.55099.30.1620.99711.5996991
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.31.2410.6178.9

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 REPLACEMENTTHROUGHOUT5EN52.55092224476799.860.196010.193370.24768RANDOM52.249
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]
1.44-2.881.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.008
r_dihedral_angle_4_deg19.475
r_dihedral_angle_3_deg15.863
r_long_range_B_other9.15
r_long_range_B_refined9.145
r_scangle_other6.724
r_dihedral_angle_1_deg6.62
r_mcangle_other6.078
r_mcangle_it6.077
r_scbond_it4.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.008
r_dihedral_angle_4_deg19.475
r_dihedral_angle_3_deg15.863
r_long_range_B_other9.15
r_long_range_B_refined9.145
r_scangle_other6.724
r_dihedral_angle_1_deg6.62
r_mcangle_other6.078
r_mcangle_it6.077
r_scbond_it4.248
r_scbond_other4.248
r_mcbond_it3.963
r_mcbond_other3.949
r_angle_refined_deg1.655
r_angle_other_deg0.998
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms16886
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing