X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VAG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.1520% 1,2-propanediol, 5% glycerol and 0.1 M NaKPO4
Crystal Properties
Matthews coefficientSolvent content
2.4750.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.181α = 90
b = 116.191β = 98.99
c = 90.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2014-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.0282DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.0529.3499.90.0928.25.272225
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1699.90.6272.15.1

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 REPLACEMENTTHROUGHOUT2vag2.0589.8668534357699.750.189710.188240.21829RANDOM47.364
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]
-0.260.33-0.60.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.281
r_sphericity_bonded29.316
r_dihedral_angle_4_deg19.167
r_dihedral_angle_3_deg13.017
r_long_range_B_refined6.325
r_long_range_B_other6.325
r_dihedral_angle_1_deg6.074
r_scangle_other3.239
r_mcangle_it2.57
r_mcangle_other2.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.281
r_sphericity_bonded29.316
r_dihedral_angle_4_deg19.167
r_dihedral_angle_3_deg13.017
r_long_range_B_refined6.325
r_long_range_B_other6.325
r_dihedral_angle_1_deg6.074
r_scangle_other3.239
r_mcangle_it2.57
r_mcangle_other2.57
r_scbond_it1.974
r_scbond_other1.971
r_mcbond_it1.575
r_mcbond_other1.575
r_angle_refined_deg1.505
r_angle_other_deg1.277
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8205
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing