X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A5J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277100 mM HEPES, 200 mM magnesium acetate, and 14% polyethylene glycol 8000, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.3347.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.254α = 90
b = 89.254β = 90
c = 105.747γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.99994ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.8952.871000.0710.025117.2939530
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.921000.0710.0750.02519.1

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 REPLACEMENTTHROUGHOUT3a5j1.8944.6737270194799.270.180730.179220.21175RANDOM21.375
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]
0.070.040.07-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.29
r_dihedral_angle_4_deg16.227
r_dihedral_angle_3_deg14.684
r_long_range_B_refined7.793
r_long_range_B_other7.708
r_dihedral_angle_1_deg6.4
r_scangle_other4.708
r_mcangle_other3.192
r_mcangle_it3.186
r_scbond_it3.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.29
r_dihedral_angle_4_deg16.227
r_dihedral_angle_3_deg14.684
r_long_range_B_refined7.793
r_long_range_B_other7.708
r_dihedral_angle_1_deg6.4
r_scangle_other4.708
r_mcangle_other3.192
r_mcangle_it3.186
r_scbond_it3.096
r_scbond_other3.096
r_mcbond_it2.079
r_mcbond_other2.059
r_angle_refined_deg1.488
r_angle_other_deg1.29
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms2296
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing