6SJJ

A new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N3E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2920.1 M HEPES buffer pH 7.5, 1.3 M sodium citrate precipitant pH 6.3, 1:1 protein:reservoir volume ratio
Crystal Properties
Matthews coefficientSolvent content
3.1661.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.85α = 90
b = 145.85β = 90
c = 385.4γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.331.5899.280.0660.9786.227.212732467.46
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.390.6910.62

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-VALUE4N3E2.331.58123350397499.280.22640.2260.2548RANDOM67.461
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]
-26.22-10.816.5119.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.3
r_dihedral_angle_4_deg16.525
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg4.542
r_angle_refined_deg1.837
r_angle_other_deg1.086
r_chiral_restr0.083
r_gen_planes_other0.014
r_gen_planes_refined0.011
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.3
r_dihedral_angle_4_deg16.525
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg4.542
r_angle_refined_deg1.837
r_angle_other_deg1.086
r_chiral_restr0.083
r_gen_planes_other0.014
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms44726
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms3465

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing