X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B3B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM Potassium phosphate monobasic/Sodium phosphate dibasic buffer (pH 6.2), 10% (w/v) polyethylene glycol (PEG) 3,000, and 10% (v/v) glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.782α = 90
b = 153.599β = 115.58
c = 110.55γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.5545.041000.1660.180.0680.99510.36.948864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.631001.1641.2590.4760.7086.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.5545.0446373249099.980.210540.207960.26022RANDOM50.374
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]
-1.11-0.43-3.393.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.984
r_long_range_B_refined8.177
r_long_range_B_other8.177
r_dihedral_angle_1_deg6.635
r_scangle_other6.167
r_dihedral_angle_2_deg5.747
r_mcangle_it5.359
r_mcangle_other5.359
r_scbond_it3.999
r_scbond_other3.998
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.984
r_long_range_B_refined8.177
r_long_range_B_other8.177
r_dihedral_angle_1_deg6.635
r_scangle_other6.167
r_dihedral_angle_2_deg5.747
r_mcangle_it5.359
r_mcangle_other5.359
r_scbond_it3.999
r_scbond_other3.998
r_mcbond_it3.57
r_mcbond_other3.569
r_angle_refined_deg1.321
r_angle_other_deg0.981
r_chiral_restr0.061
r_bond_other_d0.048
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms9180
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing