X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O0R3O0R, 1NIR
experimental modelPDB 1NIR3O0R, 1NIR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52930.1M MES, 0.2M CsCl, 12% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.4964.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.871α = 90
b = 128.606β = 106.83
c = 127.807γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors2013-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

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
13.25098.70.1170.1380.0735.63.556669
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)
13.23.3198.20.6470.6593.3

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 REPLACEMENTTHROUGHOUT3O0R, 1NIR3.249.4847760255187.670.21190.20970.254RANDOM67.021
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]
0.352.33-1.920.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg18.814
r_dihedral_angle_3_deg17.242
r_dihedral_angle_1_deg6.235
r_angle_refined_deg1.546
r_angle_other_deg0.889
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg18.814
r_dihedral_angle_3_deg17.242
r_dihedral_angle_1_deg6.235
r_angle_refined_deg1.546
r_angle_other_deg0.889
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17804
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms549

Software

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