X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2940.5 M (NH4)H2PO4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.966α = 90
b = 59.015β = 90
c = 88.651γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

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
11.71837.2399.60.074119.812.7332513
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)
11.721.8299.41.7490.6321.3412.46

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4V2Y1.7237.2330878163599.830.1960.194590.22261RANDOM37.924
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]
-0.350.93-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.504
r_dihedral_angle_3_deg13.102
r_dihedral_angle_4_deg9.929
r_dihedral_angle_1_deg7.351
r_long_range_B_refined6.625
r_long_range_B_other6.623
r_scangle_other3.74
r_mcangle_it2.485
r_mcangle_other2.484
r_scbond_it2.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.504
r_dihedral_angle_3_deg13.102
r_dihedral_angle_4_deg9.929
r_dihedral_angle_1_deg7.351
r_long_range_B_refined6.625
r_long_range_B_other6.623
r_scangle_other3.74
r_mcangle_it2.485
r_mcangle_other2.484
r_scbond_it2.439
r_scbond_other2.438
r_angle_refined_deg1.753
r_mcbond_it1.663
r_mcbond_other1.662
r_angle_other_deg1.405
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2221
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling