X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B53 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52940.1M citrate pH 5.5 11.6% PEG4K 18.4% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.2745.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.258α = 96.824
b = 58.291β = 91.36
c = 74.633γ = 104.993
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.9547.6199.70.10.99810.26.668240
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)
11.95296.70.8230.5991.23.6

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-VALUE7B532.0947.6168208349699.5340.1860.1830.236141.526
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]
-0.1592.3540.5020.7210.994-2.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.682
r_dihedral_angle_4_deg15.557
r_dihedral_angle_3_deg13.866
r_lrange_it7.229
r_lrange_other7.229
r_dihedral_angle_1_deg6.831
r_scangle_it5.936
r_scangle_other5.936
r_mcangle_it4.22
r_mcangle_other4.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.682
r_dihedral_angle_4_deg15.557
r_dihedral_angle_3_deg13.866
r_lrange_it7.229
r_lrange_other7.229
r_dihedral_angle_1_deg6.831
r_scangle_it5.936
r_scangle_other5.936
r_mcangle_it4.22
r_mcangle_other4.22
r_scbond_it3.952
r_scbond_other3.951
r_mcbond_it3.059
r_mcbond_other3.056
r_angle_refined_deg1.487
r_angle_other_deg1.331
r_symmetry_xyhbond_nbd_refined0.341
r_nbd_refined0.205
r_nbd_other0.205
r_xyhbond_nbd_refined0.194
r_symmetry_nbd_other0.175
r_symmetry_xyhbond_nbd_other0.158
r_nbtor_refined0.152
r_symmetry_nbd_refined0.133
r_symmetry_nbtor_other0.078
r_chiral_restr0.068
r_xyhbond_nbd_other0.013
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7282
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing