X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293.152.8 M Ammonium sulfate, 0.1 M citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.3647.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.241α = 90
b = 74.241β = 90
c = 222.31γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

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
11.7547.471000.0790.99714.49.26383823
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)
11.751.811000.7770.8062.79.4

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 REPLACEMENTTHROUGHOUT4WNO1.7547.4760554317799.980.171460.170130.19651RANDOM31.23
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]
0.410.41-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.445
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg13.259
r_long_range_B_refined6.529
r_long_range_B_other6.528
r_dihedral_angle_1_deg6.366
r_scangle_other4.411
r_scbond_it2.859
r_scbond_other2.859
r_mcangle_it2.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.445
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg13.259
r_long_range_B_refined6.529
r_long_range_B_other6.528
r_dihedral_angle_1_deg6.366
r_scangle_other4.411
r_scbond_it2.859
r_scbond_other2.859
r_mcangle_it2.549
r_mcangle_other2.529
r_mcbond_it1.688
r_mcbond_other1.665
r_angle_refined_deg1.541
r_angle_other_deg1.414
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.011
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 Atoms4375
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing