X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6A86 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.8 M potassium-sodium phosphate, 5% 1,3-butanediol
Crystal Properties
Matthews coefficientSolvent content
3.0359.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.778α = 90
b = 145.778β = 90
c = 39.531γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2017-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
12.45098.10.08636.75.511922
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)
12.42.440.4864.4

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 REPLACEMENTTHROUGHOUT6A862.4130.461130160397.920.180280.177280.23703RANDOM48.384
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.554
r_dihedral_angle_1_deg15.425
r_dihedral_angle_3_deg14.093
r_long_range_B_refined7.916
r_long_range_B_other7.885
r_scangle_other5.854
r_mcangle_it5.03
r_mcangle_other5.028
r_scbond_it3.918
r_scbond_other3.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.554
r_dihedral_angle_1_deg15.425
r_dihedral_angle_3_deg14.093
r_long_range_B_refined7.916
r_long_range_B_other7.885
r_scangle_other5.854
r_mcangle_it5.03
r_mcangle_other5.028
r_scbond_it3.918
r_scbond_other3.915
r_mcbond_it3.36
r_mcbond_other3.359
r_angle_refined_deg1.588
r_angle_other_deg0.938
r_chiral_restr0.069
r_bond_refined_d0.011
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_dihedral_angle_4_deg
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 Atoms1862
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing