X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.829320% Polyethylene glycol 3350, 0.2M potassium dihydrogen phosphate pH 4.8
Crystal Properties
Matthews coefficientSolvent content
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.79α = 90
b = 87.356β = 90
c = 86.766γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442015-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.95099.30.05428.95.75475713
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)
11.91.93900.2364.913.6

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 REPLACEMENTTHROUGHOUT2bjf1.945.552091261999.190.153150.151550.18533RANDOM19.805
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]
-0.220.77-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.692
r_dihedral_angle_3_deg12.711
r_dihedral_angle_4_deg11.993
r_dihedral_angle_1_deg6.474
r_long_range_B_refined5.931
r_long_range_B_other5.914
r_scangle_other4.887
r_scbond_it3.289
r_scbond_other3.252
r_mcangle_it2.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.692
r_dihedral_angle_3_deg12.711
r_dihedral_angle_4_deg11.993
r_dihedral_angle_1_deg6.474
r_long_range_B_refined5.931
r_long_range_B_other5.914
r_scangle_other4.887
r_scbond_it3.289
r_scbond_other3.252
r_mcangle_it2.326
r_mcangle_other2.326
r_angle_refined_deg1.877
r_mcbond_it1.826
r_mcbond_other1.808
r_angle_other_deg1.391
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.008
r_gen_planes_other0.006
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 Atoms5058
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing