X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HM8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229320 mM Tris-HCL, pH 7.2, 20% (v/v) PEG 400, 50 mM NaCl, 300 mM CaCl2, and 1 mM ZnCl2
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.872α = 90
b = 92.872β = 90
c = 280.703γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.94799.90.99918.210.337206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.943

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 REPLACEMENTTHROUGHOUT1HM81.946.8335343186299.920.187210.185170.22697RANDOM39.347
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]
0.790.390.79-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.498
r_dihedral_angle_4_deg23.503
r_dihedral_angle_3_deg14.093
r_dihedral_angle_1_deg7.015
r_long_range_B_refined6.467
r_long_range_B_other6.327
r_scangle_other3.15
r_mcangle_it2.448
r_mcangle_other2.448
r_scbond_it1.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.498
r_dihedral_angle_4_deg23.503
r_dihedral_angle_3_deg14.093
r_dihedral_angle_1_deg7.015
r_long_range_B_refined6.467
r_long_range_B_other6.327
r_scangle_other3.15
r_mcangle_it2.448
r_mcangle_other2.448
r_scbond_it1.982
r_scbond_other1.981
r_mcbond_it1.586
r_mcbond_other1.573
r_angle_refined_deg1.551
r_angle_other_deg1.289
r_chiral_restr0.162
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3354
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms60

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement