X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W8O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529350mM HEPES (pH7.5), 50mM KPi buffer (pH7.0), 0.63M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.3262.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.622α = 90
b = 153.622β = 90
c = 36.825γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.055099.80.0570.060.0192010.431662
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.121000.1140.120.0380.9959.83087

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 REPLACEMENTTHROUGHOUT3W8O2.0518.829932159299.680.17420.17270.203RANDOM25.532
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg22.513
r_dihedral_angle_3_deg11.274
r_dihedral_angle_1_deg5.965
r_angle_refined_deg1.477
r_angle_other_deg0.897
r_chiral_restr0.071
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.787
r_dihedral_angle_4_deg22.513
r_dihedral_angle_3_deg11.274
r_dihedral_angle_1_deg5.965
r_angle_refined_deg1.477
r_angle_other_deg0.897
r_chiral_restr0.071
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2664
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing