X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629518%(w/v) PEG3350, 0.17M Sodium thiocyanate, pH 6.0, vapor diffusion, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4750.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.961α = 90
b = 115.961β = 90
c = 385.874γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
12.653098.80.04828.33.7836621178.8
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)
12.652.7497.40.4952.12.621336

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 REPLACEMENTTHROUGHOUT3APZ2.653083456428498.570.22470.2220.274RANDOM77.543
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]
-24.33-24.3348.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.942
r_dihedral_angle_3_deg21.18
r_dihedral_angle_4_deg19.769
r_dihedral_angle_1_deg6.192
r_scangle_it2.521
r_angle_refined_deg1.472
r_scbond_it1.442
r_mcangle_it0.907
r_mcbond_it0.459
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.942
r_dihedral_angle_3_deg21.18
r_dihedral_angle_4_deg19.769
r_dihedral_angle_1_deg6.192
r_scangle_it2.521
r_angle_refined_deg1.472
r_scbond_it1.442
r_mcangle_it0.907
r_mcbond_it0.459
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19483
Nucleic Acid Atoms
Solvent Atoms695
Heterogen Atoms248

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling