X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Na citrate, 0.3 M NH4 chloride, 15-20% PEG 2000
Crystal Properties
Matthews coefficientSolvent content
3.6866.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.563α = 90
b = 104.563β = 90
c = 68.01γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9795DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9790.5599.70.070.0730.99918.211.13056427.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0299.71.4511.5210.9421.811.2

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 REPLACEMENTTHROUGHOUT5A8B290.5527817150199.970.189170.187460.2201RANDOM48.833
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]
-2.37-1.19-2.377.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.111
r_dihedral_angle_3_deg16.403
r_dihedral_angle_4_deg13.529
r_dihedral_angle_1_deg6.773
r_long_range_B_refined5.846
r_long_range_B_other5.846
r_scangle_other3.02
r_mcangle_it2.403
r_mcangle_other2.403
r_scbond_it1.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.111
r_dihedral_angle_3_deg16.403
r_dihedral_angle_4_deg13.529
r_dihedral_angle_1_deg6.773
r_long_range_B_refined5.846
r_long_range_B_other5.846
r_scangle_other3.02
r_mcangle_it2.403
r_mcangle_other2.403
r_scbond_it1.876
r_scbond_other1.876
r_angle_refined_deg1.717
r_mcbond_it1.536
r_mcbond_other1.515
r_angle_other_deg1.001
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms2042
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing