X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X8Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92990.1M MES pH6.0, 10% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.285α = 90
b = 72.555β = 90.01
c = 98.88γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 12M2012-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3572.5698.10.9947.73.146027
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4398.80.79

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 REPLACEMENTFREE R-VALUE5x8q2.3553.5343777222797.870.182830.1820.19841RANDOM53.268
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]
-43.640.0865.18-21.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.126
r_dihedral_angle_3_deg16.326
r_dihedral_angle_4_deg16.227
r_long_range_B_other12.792
r_long_range_B_refined12.79
r_scangle_other9.459
r_mcangle_other8.283
r_mcangle_it8.282
r_scbond_it7.02
r_scbond_other7.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.126
r_dihedral_angle_3_deg16.326
r_dihedral_angle_4_deg16.227
r_long_range_B_other12.792
r_long_range_B_refined12.79
r_scangle_other9.459
r_mcangle_other8.283
r_mcangle_it8.282
r_scbond_it7.02
r_scbond_other7.02
r_mcbond_it6.441
r_mcbond_other6.434
r_dihedral_angle_1_deg5.361
r_angle_refined_deg1.632
r_angle_other_deg1.284
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.008
r_bond_other_d0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7771
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing