X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BWX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1 M Bis-Tris pH 7.0, 4.0 M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
4.0969.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.311α = 90
b = 92.311β = 90
c = 222.669γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

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
12.0246.1699.90.0820.085121.119.872989
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)
12.022.0699.81.6541.6980.3820.9442.219.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7BWX2.0245.72572904364999.8740.1810.18080.17890.2157Random selection56.926
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]
0.0140.0070.014-0.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.863
r_dihedral_angle_3_deg12.32
r_lrange_it8.943
r_scangle_it8.104
r_dihedral_angle_1_deg7.912
r_scbond_it7.257
r_mcangle_it7.096
r_mcbond_it5.842
r_dihedral_angle_4_deg3.136
r_angle_refined_deg2.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.863
r_dihedral_angle_3_deg12.32
r_lrange_it8.943
r_scangle_it8.104
r_dihedral_angle_1_deg7.912
r_scbond_it7.257
r_mcangle_it7.096
r_mcbond_it5.842
r_dihedral_angle_4_deg3.136
r_angle_refined_deg2.081
r_nbtor_refined0.327
r_symmetry_nbd_refined0.276
r_nbd_refined0.216
r_chiral_restr0.144
r_xyhbond_nbd_refined0.143
r_symmetry_xyhbond_nbd_refined0.141
r_gen_planes_refined0.012
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4239
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing