X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I8D5I8D, 5UZ8
experimental modelPDB 5UZ85I8D, 5UZ8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.05 M TRIS pH 8.5 0.5 M NaCl 10% PEG-4000
Crystal Properties
Matthews coefficientSolvent content
3.0159.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.714α = 90
b = 166.806β = 102.53
c = 47.93γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2016-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBERIGAKU MICROMAX-0031.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.5494.0899.40.165.952.91085668
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)
13.543.6199.60.4252.22.7

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 REPLACEMENTTHROUGHOUT5I8D, 5UZ83.5494.0810174577980.3050.3030.346RANDOM66.92
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]
10.63.71-10.8-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.45
r_dihedral_angle_3_deg16.894
r_dihedral_angle_4_deg12.551
r_dihedral_angle_1_deg9.137
r_angle_refined_deg1.349
r_angle_other_deg0.86
r_long_range_B_refined0.082
r_long_range_B_other0.081
r_chiral_restr0.079
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.45
r_dihedral_angle_3_deg16.894
r_dihedral_angle_4_deg12.551
r_dihedral_angle_1_deg9.137
r_angle_refined_deg1.349
r_angle_other_deg0.86
r_long_range_B_refined0.082
r_long_range_B_other0.081
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4658
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing