X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DSM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.9357.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.315α = 90
b = 59.078β = 103.865
c = 101.544γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96858DiamondI24

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
11.7259.0899.40.1080.1470.0990.98863.597918
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)
11.721.750.7360.9990.6720.5573.6

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3DSM1.7255.07297856484999.4550.1810.17870.222719.783
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]
0.3630.4550.09-0.604
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.543
r_dihedral_angle_4_deg20.191
r_dihedral_angle_3_deg11.472
r_dihedral_angle_1_deg7.815
r_lrange_it4.094
r_lrange_other3.622
r_scangle_it2.961
r_scangle_other2.936
r_scbond_it2.429
r_scbond_other2.417
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.543
r_dihedral_angle_4_deg20.191
r_dihedral_angle_3_deg11.472
r_dihedral_angle_1_deg7.815
r_lrange_it4.094
r_lrange_other3.622
r_scangle_it2.961
r_scangle_other2.936
r_scbond_it2.429
r_scbond_other2.417
r_mcangle_it2.384
r_mcangle_other2.384
r_mcbond_it1.896
r_mcbond_other1.891
r_angle_refined_deg1.694
r_rigid_bond_restr1.356
r_angle_other_deg1.274
r_symmetry_nbd_refined0.258
r_nbd_other0.212
r_symmetry_nbd_other0.179
r_nbd_refined0.177
r_xyhbond_nbd_refined0.174
r_nbtor_refined0.172
r_symmetry_xyhbond_nbd_refined0.154
r_symmetry_nbtor_other0.074
r_ncsr_local_group_10.067
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5480
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms208

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing