X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A9TPDB ENTRY 5A9T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7
Crystal Properties
Matthews coefficientSolvent content
2.9458

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.822α = 108.75
b = 80.255β = 108.78
c = 123.895γ = 90.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 6M2015-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.3575.4897.40.22.91.81110532
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)
12.352.3997.10.551.21.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5A9T2.35110.32105360565697.350.205630.204310.22902RANDOM38.32
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]
1.13-0.32-0.420.69-0.25-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.514
r_dihedral_angle_4_deg21.718
r_dihedral_angle_3_deg15.965
r_dihedral_angle_1_deg5.436
r_mcangle_it3.576
r_scbond_it2.77
r_mcbond_it2.353
r_mcbond_other2.352
r_angle_refined_deg1.701
r_angle_other_deg1.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.514
r_dihedral_angle_4_deg21.718
r_dihedral_angle_3_deg15.965
r_dihedral_angle_1_deg5.436
r_mcangle_it3.576
r_scbond_it2.77
r_mcbond_it2.353
r_mcbond_other2.352
r_angle_refined_deg1.701
r_angle_other_deg1.349
r_chiral_restr0.094
r_bond_refined_d0.012
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.005
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16864
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms488

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing