X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6II66II6 AND 6IMP
experimental modelPDB 6IMP6II6 AND 6IMP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27722% PEG 4000, 0.1M Tris-HCl (pH 8.5), 0.2M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.6152.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.215α = 90
b = 108.593β = 90
c = 334.737γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152018-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9794PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.55089.95.15.734303
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.561.5090.5810.562

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 REPLACEMENTTHROUGHOUT6II6 AND 6IMP3.549.629984151477.50.287060.285030.3274RANDOM59.345
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]
-0.60.84-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.085
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg16.164
r_long_range_B_refined9.652
r_long_range_B_other9.651
r_dihedral_angle_1_deg8.166
r_mcangle_it5.344
r_mcangle_other5.344
r_scangle_other4.413
r_mcbond_it3.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.085
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg16.164
r_long_range_B_refined9.652
r_long_range_B_other9.651
r_dihedral_angle_1_deg8.166
r_mcangle_it5.344
r_mcangle_other5.344
r_scangle_other4.413
r_mcbond_it3.067
r_mcbond_other3.066
r_scbond_it2.395
r_scbond_other2.395
r_angle_refined_deg1.195
r_angle_other_deg0.808
r_chiral_restr0.073
r_bond_refined_d0.01
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
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 Atoms17825
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
REFMACrefinement