X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293.1518 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.2545.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.85α = 90
b = 56.07β = 90
c = 108.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.872600ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.3921081000.0880.0950.03514.67.24455444554
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.391.471000.4180.4180.1681.87.16395

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 REPLACEMENTTHROUGHOUT3TYI1.3926.3842297224599.970.13180.13030.1597RANDOM10.634
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]
-0.44-0.140.58
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.968
r_dihedral_angle_2_deg30.745
r_dihedral_angle_4_deg28.47
r_sphericity_bonded17.854
r_rigid_bond_restr14.319
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.185
r_angle_refined_deg1.319
r_angle_other_deg1.16
r_mcangle_it0.921
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free30.968
r_dihedral_angle_2_deg30.745
r_dihedral_angle_4_deg28.47
r_sphericity_bonded17.854
r_rigid_bond_restr14.319
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg6.185
r_angle_refined_deg1.319
r_angle_other_deg1.16
r_mcangle_it0.921
r_mcbond_it0.754
r_mcbond_other0.75
r_chiral_restr0.089
r_gen_planes_other0.013
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1690
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction