X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YN7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52970.1 M HEPES pH 7.5, 1.8 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2846.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.668α = 90
b = 119.668β = 90
c = 85.776γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU2015-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54187

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
13.25098.90.1645.16.910704
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)
13.23.261000.4867510

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 REPLACEMENTTHROUGHOUT4YN73.234.88890445086.730.24790.24630.2808RANDOM94.62
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]
-2.18-2.184.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.21
r_dihedral_angle_3_deg16.761
r_dihedral_angle_4_deg13.956
r_dihedral_angle_1_deg5.802
r_angle_refined_deg1.443
r_angle_other_deg0.849
r_chiral_restr0.064
r_bond_refined_d0.01
r_bond_other_d0.007
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.21
r_dihedral_angle_3_deg16.761
r_dihedral_angle_4_deg13.956
r_dihedral_angle_1_deg5.802
r_angle_refined_deg1.443
r_angle_other_deg0.849
r_chiral_restr0.064
r_bond_refined_d0.01
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4584
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing