X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WGT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4650.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.402α = 90
b = 270.896β = 90
c = 135.429γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDDECTRIS EIGER X 4M2015-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.10Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1349.171000.10.040.99715.27.3621923
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)
133.161000.4570.9264.47.7

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 REPLACEMENTTHROUGHOUT3WGT349.1759226294399.950.169450.165190.25335RANDOM62.635
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]
4.840.03-4.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.568
r_dihedral_angle_3_deg17.911
r_dihedral_angle_4_deg15.845
r_long_range_B_refined8.181
r_long_range_B_other8.181
r_dihedral_angle_1_deg7.126
r_mcangle_it5.891
r_mcangle_other5.89
r_scangle_other5.162
r_mcbond_it3.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.568
r_dihedral_angle_3_deg17.911
r_dihedral_angle_4_deg15.845
r_long_range_B_refined8.181
r_long_range_B_other8.181
r_dihedral_angle_1_deg7.126
r_mcangle_it5.891
r_mcangle_other5.89
r_scangle_other5.162
r_mcbond_it3.607
r_mcbond_other3.607
r_scbond_it3.132
r_scbond_other3.131
r_angle_refined_deg1.488
r_angle_other_deg0.97
r_chiral_restr0.077
r_gen_planes_refined0.016
r_bond_refined_d0.01
r_gen_planes_other0.005
r_bond_other_d0.002
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 Atoms21640
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms630

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing