X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FYOPDB ENTRY 5FYO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS
Crystal Properties
Matthews coefficientSolvent content
1.9737.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.21α = 90
b = 135.21β = 90
c = 112.47γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-02MSINGLE 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
11.1767.6199.90.0817.211.73460882

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 5FYO1.1767.613287191724399.940.125940.12480.1476RANDOM12.925
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.003
r_dihedral_angle_2_deg35.01
r_rigid_bond_restr22.483
r_dihedral_angle_4_deg16.249
r_dihedral_angle_3_deg11.188
r_sphericity_bonded11.103
r_dihedral_angle_1_deg6.309
r_long_range_B_refined4.852
r_long_range_B_other4.679
r_scangle_other3.168
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.003
r_dihedral_angle_2_deg35.01
r_rigid_bond_restr22.483
r_dihedral_angle_4_deg16.249
r_dihedral_angle_3_deg11.188
r_sphericity_bonded11.103
r_dihedral_angle_1_deg6.309
r_long_range_B_refined4.852
r_long_range_B_other4.679
r_scangle_other3.168
r_scbond_it2.781
r_scbond_other2.781
r_angle_other_deg2.153
r_mcangle_other1.873
r_mcangle_it1.872
r_mcbond_it1.706
r_mcbond_other1.704
r_angle_refined_deg1.552
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.008
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 Atoms9131
Nucleic Acid Atoms
Solvent Atoms1843
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing