X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Ethylene glycol, HEPES, PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.1141.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.02α = 99.3
b = 81.05β = 101.5
c = 106.13γ = 87.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.0548.8497.60.080.0950.99811.533.49210075330.924
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.196.90.4960.5840.8352.783.57

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 REPLACEMENTTHROUGHOUT5ZFS2.0548.8495721503197.680.16580.16180.2414RANDOM26.886
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]
-0.450.43-0.230.610.38-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.442
r_dihedral_angle_4_deg16.557
r_dihedral_angle_3_deg13.388
r_rigid_bond_restr8.847
r_dihedral_angle_1_deg6.374
r_angle_other_deg1.191
r_angle_refined_deg1.147
r_chiral_restr0.042
r_bond_refined_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.442
r_dihedral_angle_4_deg16.557
r_dihedral_angle_3_deg13.388
r_rigid_bond_restr8.847
r_dihedral_angle_1_deg6.374
r_angle_other_deg1.191
r_angle_refined_deg1.147
r_chiral_restr0.042
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13288
Nucleic Acid Atoms
Solvent Atoms939
Heterogen Atoms168

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing