X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.7527710 mg/ml of protein, 0.46 M Na citrate. Drops are set in a 1:1 ratio
Crystal Properties
Matthews coefficientSolvent content
4.2170.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.73α = 90
b = 246.074β = 90
c = 261.812γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.244.5899.90.1340.9917.28.3786559
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.281.310.731.8

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 REPLACEMENTTHROUGHOUT6EOO3.244.5882126432399.890.185990.183950.22478RANDOM84.864
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]
-0.313.55-3.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.202
r_dihedral_angle_4_deg16.711
r_dihedral_angle_3_deg16.652
r_long_range_B_refined8.493
r_long_range_B_other8.493
r_dihedral_angle_1_deg6.856
r_scangle_other5.445
r_mcangle_it5.348
r_mcangle_other5.348
r_mcbond_it3.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.202
r_dihedral_angle_4_deg16.711
r_dihedral_angle_3_deg16.652
r_long_range_B_refined8.493
r_long_range_B_other8.493
r_dihedral_angle_1_deg6.856
r_scangle_other5.445
r_mcangle_it5.348
r_mcangle_other5.348
r_mcbond_it3.191
r_mcbond_other3.191
r_scbond_it3.153
r_scbond_other3.153
r_angle_refined_deg0.984
r_angle_other_deg0.284
r_chiral_restr0.04
r_bond_refined_d0.003
r_gen_planes_refined0.003
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 Atoms20388
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing