X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B5R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION729120mM Sodium bromide, 0.1M Hepes sodium pH7.0, 1.5M Sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.5952.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.886α = 90
b = 86.165β = 90
c = 112.145γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152016-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.979SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6468.33980.1940.19413.256.413984
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)
12.642.797.60.6940.9112.226

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 REPLACEMENTTHROUGHOUT5B5R2.6468.331327670898.260.2380.235440.2856RANDOM51.198
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]
-2.72.77-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.183
r_dihedral_angle_3_deg16.137
r_dihedral_angle_4_deg14.319
r_long_range_B_refined7.051
r_long_range_B_other7.051
r_dihedral_angle_1_deg6.623
r_scangle_other4.341
r_mcangle_it4.193
r_mcangle_other4.193
r_scbond_it2.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.183
r_dihedral_angle_3_deg16.137
r_dihedral_angle_4_deg14.319
r_long_range_B_refined7.051
r_long_range_B_other7.051
r_dihedral_angle_1_deg6.623
r_scangle_other4.341
r_mcangle_it4.193
r_mcangle_other4.193
r_scbond_it2.591
r_scbond_other2.585
r_mcbond_it2.542
r_mcbond_other2.527
r_angle_refined_deg1.417
r_angle_other_deg0.961
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2877
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing