X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WNO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1522.5% PEG 3350, 0.2 M sodium citrate, pH 5.9, 0.1 M bis-tris, pH 5.75, 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.9358.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.006α = 90
b = 117.006β = 90
c = 141.485γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

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
12.4858.51000.1360.99811.59.84024047
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)
12.482.611000.9980.7112.29.8

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 REPLACEMENTTHROUGHOUT4WNO2.4858.538110208899.980.197760.195590.2366RANDOM57.774
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]
-0.69-0.35-0.692.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.51
r_dihedral_angle_4_deg23.842
r_dihedral_angle_3_deg15.849
r_dihedral_angle_1_deg7.029
r_long_range_B_refined6.726
r_long_range_B_other6.725
r_mcangle_it3.999
r_mcangle_other3.998
r_scangle_other3.71
r_mcbond_it2.285
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.51
r_dihedral_angle_4_deg23.842
r_dihedral_angle_3_deg15.849
r_dihedral_angle_1_deg7.029
r_long_range_B_refined6.726
r_long_range_B_other6.725
r_mcangle_it3.999
r_mcangle_other3.998
r_scangle_other3.71
r_mcbond_it2.285
r_mcbond_other2.285
r_scbond_it2.134
r_scbond_other2.134
r_angle_refined_deg1.12
r_angle_other_deg0.853
r_chiral_restr0.06
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms6322
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing