X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529325 % PEG-3350 W/V, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.129α = 90
b = 63.7β = 90
c = 144.118γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.3438.3597.30.0382317.853.993866
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)
11.341.3981.80.47522.483

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 REPLACEMENTTHROUGHOUT3ATV1.3438.3591861200097.30.1320.1310.154RANDOM22.46
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]
-0.050.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free55.963
r_dihedral_angle_2_deg34.951
r_sphericity_bonded28.344
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg12.128
r_long_range_B_refined7.394
r_rigid_bond_restr6.679
r_dihedral_angle_1_deg5.682
r_scbond_it4.398
r_mcangle_it2.583
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free55.963
r_dihedral_angle_2_deg34.951
r_sphericity_bonded28.344
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg12.128
r_long_range_B_refined7.394
r_rigid_bond_restr6.679
r_dihedral_angle_1_deg5.682
r_scbond_it4.398
r_mcangle_it2.583
r_mcbond_it2.205
r_angle_refined_deg1.998
r_chiral_restr0.142
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2930
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction