X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I6U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72951:1 ratio mix of protein solution (~12 mg/ml protein in 20 mM Tris-HCl, 150 mM NaCl, 10 mM dithiothreitol (DTT), 3% (v/v) glycerol, pH 8.0 and well bufffer (100 mM NaHepes, 300 mM Ammonium Tartrate, 22% PEG 3350, pH 7.0). Crystals were flash frozen in crystallization buffer supplemented with 16-20% (v/v) glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5752.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.2α = 84.1
b = 114.7β = 81.2
c = 123γ = 80.7
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152006-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-EAPS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.253096.20.0421.860983

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 REPLACEMENTTHROUGHOUT3I6U3.253056117175590.80.2520.2510.287RANDOM137.5
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]
-0.26-0.341.73-3.09-3.453.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.202
r_dihedral_angle_4_deg21.623
r_dihedral_angle_3_deg19.937
r_dihedral_angle_1_deg5.446
r_scangle_it4.357
r_scbond_it2.596
r_mcangle_it2.574
r_mcbond_it1.442
r_angle_refined_deg1.138
r_symmetry_hbond_refined0.626
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.202
r_dihedral_angle_4_deg21.623
r_dihedral_angle_3_deg19.937
r_dihedral_angle_1_deg5.446
r_scangle_it4.357
r_scbond_it2.596
r_mcangle_it2.574
r_mcbond_it1.442
r_angle_refined_deg1.138
r_symmetry_hbond_refined0.626
r_symmetry_vdw_refined0.619
r_nbtor_refined0.31
r_nbd_refined0.218
r_xyhbond_nbd_refined0.144
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24560
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement