X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS (pH 7) 12-15% PEG3350 10 mM TDP-Qui3N 1 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.1643.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.824α = 90
b = 56.644β = 90.01
c = 124.549γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.455098.20.0760.07693.2261560
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)
11.451.5593.80.371.9247910

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 REPLACEMENTTHROUGHOUT2u1z1.4529.922485921295298.160.128530.127240.1534RANDOM12.901
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]
2.35-1.232.34-4.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.029
r_dihedral_angle_4_deg16.852
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg6.772
r_long_range_B_refined5.4
r_long_range_B_other5.4
r_scangle_other4.288
r_scbond_it3.029
r_scbond_other3.029
r_mcangle_it2.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.029
r_dihedral_angle_4_deg16.852
r_dihedral_angle_3_deg14.364
r_dihedral_angle_1_deg6.772
r_long_range_B_refined5.4
r_long_range_B_other5.4
r_scangle_other4.288
r_scbond_it3.029
r_scbond_other3.029
r_mcangle_it2.239
r_mcangle_other2.239
r_mcbond_it1.754
r_mcbond_other1.751
r_angle_refined_deg1.731
r_angle_other_deg0.796
r_chiral_restr0.114
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.001
r_bond_other_d
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 Atoms11791
Nucleic Acid Atoms
Solvent Atoms1593
Heterogen Atoms244

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing