X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EANPDB ENTRY 3EAN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529345 % MPD and 100 mM Tris-Cl buffer , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.1470.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.99α = 90
b = 162.99β = 90
c = 236.44γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
12.47097.30.0948.53.9137497137497
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)
12.42.53900.671.73.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3EAN2.460.67134215134215709599.590.16150.16150.160150.18708RANDOM61.197
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]
0.540.540.54-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.047
r_dihedral_angle_4_deg19.246
r_dihedral_angle_3_deg13.721
r_dihedral_angle_1_deg5.917
r_angle_refined_deg1.816
r_angle_other_deg1.202
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.047
r_dihedral_angle_4_deg19.246
r_dihedral_angle_3_deg13.721
r_dihedral_angle_1_deg5.917
r_angle_refined_deg1.816
r_angle_other_deg1.202
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.008
r_gen_planes_other0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14940
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms296

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling