X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.8 M potassium-sodium phosphate (pH 7.0), 5% 1,3-butanediol
Crystal Properties
Matthews coefficientSolvent content
3.0259.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.28α = 90
b = 145.28β = 90
c = 39.625γ = 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-5A1.000Photon 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
11.85098.90.05342.25.628520
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)
11.81.830.391

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 REPLACEMENTTHROUGHOUT5XZK1.85026967135698.070.198260.195750.24852RANDOM33.655
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_deg30.597
r_dihedral_angle_3_deg15.61
r_long_range_B_refined7.823
r_long_range_B_other7.806
r_dihedral_angle_1_deg6.361
r_scangle_other5.509
r_mcangle_other4.786
r_mcangle_it4.785
r_scbond_it4.05
r_scbond_other3.987
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.597
r_dihedral_angle_3_deg15.61
r_long_range_B_refined7.823
r_long_range_B_other7.806
r_dihedral_angle_1_deg6.361
r_scangle_other5.509
r_mcangle_other4.786
r_mcangle_it4.785
r_scbond_it4.05
r_scbond_other3.987
r_mcbond_it3.39
r_mcbond_other3.372
r_angle_refined_deg2.255
r_angle_other_deg1.099
r_chiral_restr0.125
r_bond_refined_d0.031
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms1855
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms24

Software

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