X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529315% v/v PEG 400, 50mM Tris-HCl (pH8.5), 50mM KPi buffer (pH7.0), 100mM MgCl2, 15% v/v PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.141.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.652α = 90
b = 83.46β = 89.95
c = 83.489γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-11-09MSINGLE 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
11.455096.20.0280.0340.01916.63.1107752
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)
11.451.5800.2040.2550.1510.9142.48884

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 REPLACEMENTTHROUGHOUT3W8O1.4519.48101412534796.390.1940.19280.2177RANDOM13.68
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_deg31.181
r_dihedral_angle_4_deg18.044
r_dihedral_angle_3_deg10.698
r_dihedral_angle_1_deg5.874
r_angle_refined_deg1.48
r_angle_other_deg0.929
r_chiral_restr0.071
r_bond_refined_d0.008
r_bond_other_d0.007
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.181
r_dihedral_angle_4_deg18.044
r_dihedral_angle_3_deg10.698
r_dihedral_angle_1_deg5.874
r_angle_refined_deg1.48
r_angle_other_deg0.929
r_chiral_restr0.071
r_bond_refined_d0.008
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5340
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms296

Software

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