X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29312% PEG 3,350, 0.15 M malic acid
Crystal Properties
Matthews coefficientSolvent content
2.6553.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.969α = 90
b = 70.969β = 90
c = 141.076γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS 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
12.583099.90.14613.696.724572
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)
12.62.690.74

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 REPLACEMENTTHROUGHOUT6JNL2.630186141027850.2510.2510.265RANDOM54.33
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]
-2.19-2.194.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_4_deg20.819
r_dihedral_angle_3_deg19.515
r_long_range_B_refined12.396
r_dihedral_angle_1_deg7.633
r_mcangle_it6.832
r_mcbond_it4.261
r_scbond_it3.989
r_angle_refined_deg1.559
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.764
r_dihedral_angle_4_deg20.819
r_dihedral_angle_3_deg19.515
r_long_range_B_refined12.396
r_dihedral_angle_1_deg7.633
r_mcangle_it6.832
r_mcbond_it4.261
r_scbond_it3.989
r_angle_refined_deg1.559
r_chiral_restr0.104
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2940
Nucleic Acid Atoms1948
Solvent Atoms
Heterogen Atoms12

Software

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