X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2900.2 M magnesium acetate tetrahydrate, 0.1 M Tris HCl pH 6.2 and 15% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5551.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.076α = 90
b = 63.446β = 89.99
c = 108.573γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

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
11.38108.5798.30.04525.73.9145157
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.45

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 REPLACEMENTTHROUGHOUT5XKO1.38108.57136748714497.420.128850.127650.15261RANDOM18.148
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg19.749
r_dihedral_angle_3_deg12.86
r_long_range_B_refined12.853
r_long_range_B_other12.686
r_dihedral_angle_1_deg5.34
r_scangle_other3.456
r_scbond_it2.263
r_scbond_other2.263
r_mcangle_it2.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg19.749
r_dihedral_angle_3_deg12.86
r_long_range_B_refined12.853
r_long_range_B_other12.686
r_dihedral_angle_1_deg5.34
r_scangle_other3.456
r_scbond_it2.263
r_scbond_other2.263
r_mcangle_it2.056
r_mcangle_other2.055
r_angle_refined_deg1.825
r_mcbond_it1.378
r_mcbond_other1.378
r_angle_other_deg1.027
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4782
Nucleic Acid Atoms
Solvent Atoms1265
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
Auto-Rickshawphasing