X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L6R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293100mM HEPES, pH7.0, 200mM potassium phospphate monobasic, 20% PEG500DME, 10 mM gly-gly-glysine
Crystal Properties
Matthews coefficientSolvent content
3.6866.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.46α = 90
b = 248.79β = 90.16
c = 93.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.195092.83.12.849677

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 REPLACEMENTTHROUGHOUT4L6R3.1946.9248212254794.080.20660.205260.23148RANDOM116.895
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]
-13.933.56-5.6619.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.187
r_dihedral_angle_3_deg19.332
r_long_range_B_refined13.422
r_long_range_B_other13.422
r_dihedral_angle_4_deg12.429
r_mcangle_it7.676
r_mcangle_other7.675
r_scangle_other6.98
r_dihedral_angle_1_deg4.781
r_mcbond_it4.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.187
r_dihedral_angle_3_deg19.332
r_long_range_B_refined13.422
r_long_range_B_other13.422
r_dihedral_angle_4_deg12.429
r_mcangle_it7.676
r_mcangle_other7.675
r_scangle_other6.98
r_dihedral_angle_1_deg4.781
r_mcbond_it4.764
r_mcbond_other4.764
r_scbond_it4.259
r_scbond_other4.258
r_angle_refined_deg1.397
r_angle_other_deg1.208
r_chiral_restr0.075
r_bond_refined_d0.011
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms14762
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms278

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing