X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YNA2YNA chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320.3 mg/mL protein; well solution: Morpheus Screen Condition H10, 0.1M Tris-Bis Tris pH 8.5, 0.1M amino acids, 30% v/v ethylene glycol-polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
2.652.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.695α = 90
b = 91.447β = 106.64
c = 120.339γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2014-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.555099.90.03427.13.8197587
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)
11.551.591000.4123.6

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 REPLACEMENTTHROUGHOUT2YNA chain A1.5550187620995299.770.186960.185470.21552RANDOM16.709
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]
0.06-0.510.46-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg14.987
r_dihedral_angle_3_deg12.949
r_dihedral_angle_1_deg6.359
r_scangle_it3.261
r_scbond_it2.125
r_mcangle_it1.413
r_angle_refined_deg1.397
r_angle_other_deg0.898
r_mcbond_it0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg14.987
r_dihedral_angle_3_deg12.949
r_dihedral_angle_1_deg6.359
r_scangle_it3.261
r_scbond_it2.125
r_mcangle_it1.413
r_angle_refined_deg1.397
r_angle_other_deg0.898
r_mcbond_it0.803
r_mcbond_other0.206
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9266
Nucleic Acid Atoms
Solvent Atoms1638
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement