X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZV2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2291A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) was improved by three rounds of serial microseeding; the crystals were crushed and serially diluted in the precipitant, and new hanging drops were prepared by mixing 2 uL protein and 2 uL microseed suspension.
Crystal Properties
Matthews coefficientSolvent content
2.4649.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.03α = 90
b = 68.88β = 90
c = 318.63γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9501Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.5933.6699.40.1580.9938.26.83310629.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.592.7199.30.7750.7552.46.9

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 REPLACEMENTTHROUGHOUT4ZV22.5933.1931387168698.870.255180.253480.28733RANDOM43.419
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]
2.350.55-2.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.911
r_dihedral_angle_3_deg18.623
r_dihedral_angle_4_deg13.699
r_dihedral_angle_1_deg6.038
r_long_range_B_refined3.106
r_long_range_B_other3.103
r_mcangle_it1.86
r_mcangle_other1.859
r_scangle_other1.5
r_angle_refined_deg1.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.911
r_dihedral_angle_3_deg18.623
r_dihedral_angle_4_deg13.699
r_dihedral_angle_1_deg6.038
r_long_range_B_refined3.106
r_long_range_B_other3.103
r_mcangle_it1.86
r_mcangle_other1.859
r_scangle_other1.5
r_angle_refined_deg1.372
r_angle_other_deg1.195
r_mcbond_other1.046
r_mcbond_it1.045
r_scbond_it0.836
r_scbond_other0.836
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.006
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 Atoms6937
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing