X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JNL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29316% PEG 3,350, 0.03 M citrate acid, 0.07 M Bis-Tris propane pH 7.6
Crystal Properties
Matthews coefficientSolvent content
3.6666.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.516α = 90
b = 88.516β = 90
c = 72.33γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 S 6M2017-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

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
12.05301000.1024.24112.335297
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)
12.052.121.02

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 REPLACEMENTTHROUGHOUT6JNL2.053031212166693.20.2010.20.228RANDOM28.27
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]
-0.23-0.230.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg19.956
r_dihedral_angle_3_deg18.738
r_dihedral_angle_1_deg6.535
r_long_range_B_other6.356
r_long_range_B_refined6.35
r_scangle_other4.837
r_mcangle_it3.927
r_mcangle_other3.926
r_scbond_it3.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg19.956
r_dihedral_angle_3_deg18.738
r_dihedral_angle_1_deg6.535
r_long_range_B_other6.356
r_long_range_B_refined6.35
r_scangle_other4.837
r_mcangle_it3.927
r_mcangle_other3.926
r_scbond_it3.362
r_scbond_other3.361
r_mcbond_it2.722
r_mcbond_other2.713
r_angle_refined_deg2.092
r_angle_other_deg1.41
r_chiral_restr0.114
r_bond_refined_d0.024
r_gen_planes_refined0.016
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1478
Nucleic Acid Atoms974
Solvent Atoms168
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing