X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DVZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8529815-25% PEG3350 and 0.1 M Na HEPES pH 7.85
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.952α = 90
b = 107.822β = 90
c = 159.772γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.474098.40.0310.99912.14.3243063
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.471.4977.30.2844.8

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 REPLACEMENTTHROUGHOUT5DVZ1.47402300041202898.350.199980.199260.21368RANDOM24.493
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]
1.92-0.38-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.698
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg11.523
r_dihedral_angle_1_deg5.405
r_long_range_B_refined4.117
r_long_range_B_other4.062
r_angle_refined_deg1.141
r_angle_other_deg0.865
r_mcangle_it0.345
r_mcangle_other0.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.698
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg11.523
r_dihedral_angle_1_deg5.405
r_long_range_B_refined4.117
r_long_range_B_other4.062
r_angle_refined_deg1.141
r_angle_other_deg0.865
r_mcangle_it0.345
r_mcangle_other0.345
r_scangle_other0.218
r_mcbond_it0.184
r_mcbond_other0.184
r_scbond_it0.117
r_scbond_other0.115
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11567
Nucleic Acid Atoms
Solvent Atoms854
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing