X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE
Crystal Properties
Matthews coefficientSolvent content
1.9436.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.285α = 90
b = 73.737β = 90
c = 77.613γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3742.5997.70.0390.02620.33.683133
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.41997.10.488

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 REPLACEMENTTHROUGHOUT5ZGU1.3742.5979355371797.380.133670.132250.16334RANDOM14.042
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]
2.07-1.07-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.831
r_sphericity_free22.131
r_dihedral_angle_4_deg17.928
r_dihedral_angle_3_deg14.377
r_sphericity_bonded13.405
r_dihedral_angle_1_deg6.736
r_rigid_bond_restr5.912
r_scangle_other4.532
r_scbond_it4.18
r_scbond_other4.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.831
r_sphericity_free22.131
r_dihedral_angle_4_deg17.928
r_dihedral_angle_3_deg14.377
r_sphericity_bonded13.405
r_dihedral_angle_1_deg6.736
r_rigid_bond_restr5.912
r_scangle_other4.532
r_scbond_it4.18
r_scbond_other4.179
r_long_range_B_refined3.739
r_long_range_B_other3.608
r_mcangle_it2.393
r_mcangle_other2.392
r_mcbond_it2.079
r_mcbond_other2.065
r_angle_refined_deg1.991
r_angle_other_deg1.187
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3366
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing