X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529117.5 % polyethylene glycol 4,000, 0.1 M citrate pH 5.5, 20 % (v/v) 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.2545.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.862α = 90
b = 143.862β = 90
c = 59.722γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.999871SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9520.199.90.310.320.9988.8220.351859-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.071003.523.620.647119.7

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 REPLACEMENTTHROUGHOUT6GRE1.9520.149227259199.80.230180.22850.26189RANDOM41.671
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]
0.560.280.56-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.346
r_dihedral_angle_3_deg17.328
r_dihedral_angle_4_deg14.392
r_dihedral_angle_1_deg6.776
r_long_range_B_refined4.154
r_long_range_B_other4.122
r_scangle_other1.756
r_mcangle_it1.619
r_mcangle_other1.618
r_angle_refined_deg1.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.346
r_dihedral_angle_3_deg17.328
r_dihedral_angle_4_deg14.392
r_dihedral_angle_1_deg6.776
r_long_range_B_refined4.154
r_long_range_B_other4.122
r_scangle_other1.756
r_mcangle_it1.619
r_mcangle_other1.618
r_angle_refined_deg1.148
r_scbond_it1.063
r_scbond_other1.063
r_mcbond_it0.926
r_mcbond_other0.926
r_angle_other_deg0.845
r_chiral_restr0.055
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms4791
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing