X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729321% (w/v) PEG3350 2.1% (w/v) 1,6-hexanediol 150 mM NaCl 50 mM HEPES-NaOH, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5651.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.494α = 90
b = 87.83β = 105.23
c = 104.578γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.10Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
11.8100.9198.40.0580.0640.0270.0270.99918.35.3135702
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.997.30.3940.4350.1820.1820.9114.75.5

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 REPLACEMENTTHROUGHOUT5XZQ1.8100.91128976670298.240.17380.172490.19871RANDOM22.81
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]
0.55-0.090.48-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.192
r_dihedral_angle_4_deg14.403
r_dihedral_angle_3_deg14.306
r_dihedral_angle_1_deg6.164
r_long_range_B_refined5.399
r_long_range_B_other4.993
r_scangle_other2.197
r_mcangle_it2.104
r_mcangle_other2.104
r_angle_refined_deg1.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.192
r_dihedral_angle_4_deg14.403
r_dihedral_angle_3_deg14.306
r_dihedral_angle_1_deg6.164
r_long_range_B_refined5.399
r_long_range_B_other4.993
r_scangle_other2.197
r_mcangle_it2.104
r_mcangle_other2.104
r_angle_refined_deg1.305
r_scbond_it1.297
r_scbond_other1.297
r_mcbond_it1.219
r_mcbond_other1.218
r_angle_other_deg0.894
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms10329
Nucleic Acid Atoms
Solvent Atoms1743
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing