X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 15 % PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.1360.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.24α = 90
b = 111.38β = 90
c = 143.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.447.8399.970.1180.1220.0310.99915.914.744778
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)
12.42.4496.551.4871.5610.4630.4991.410.8

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 REPLACEMENTTHROUGHOUT5U6Q2.444.0342501221199.80.193030.190740.236RANDOM57.395
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]
0.37-0.29-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.141
r_dihedral_angle_3_deg15.957
r_dihedral_angle_4_deg13.075
r_dihedral_angle_1_deg7.967
r_long_range_B_refined6.816
r_long_range_B_other6.815
r_scangle_other4.985
r_mcangle_it3.956
r_mcangle_other3.955
r_scbond_it3.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.141
r_dihedral_angle_3_deg15.957
r_dihedral_angle_4_deg13.075
r_dihedral_angle_1_deg7.967
r_long_range_B_refined6.816
r_long_range_B_other6.815
r_scangle_other4.985
r_mcangle_it3.956
r_mcangle_other3.955
r_scbond_it3.256
r_scbond_other3.255
r_mcbond_it2.635
r_mcbond_other2.634
r_angle_refined_deg1.532
r_angle_other_deg1.234
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms6296
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing