X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D06 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52936.8 mg/ml CHI 50 mM Na phosphate, pH 6.8. Precipitant 1.5 M (NH4)2SO4, 0.2 M NaCl, 0.1 M HEPES pH 7.5. Soaking for 10 min in 2.5 mM taxifolin (2.5% ethanol)
Crystal Properties
Matthews coefficientSolvent content
4.8875

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 186.359α = 90
b = 204.683β = 90
c = 561.904γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922016-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.9533.9698.80.2893.923.9222202547.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.0595.10.763.06

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4D06333.955211050427298.8330.2490.24890.250.26810.2758.08
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]
0.868-0.211-0.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.371
r_dihedral_angle_3_deg14.895
r_dihedral_angle_2_deg10.163
r_dihedral_angle_1_deg7.771
r_lrange_it6.62
r_lrange_other6.62
r_scangle_it3.738
r_scangle_other3.649
r_mcangle_it3.34
r_mcangle_other3.34
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms38166
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms1083

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing