X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JZJ4JZJ, 1JLI
experimental modelPDB 1JLI4JZJ, 1JLI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.829320% PEG 8000, 200 mM NaCl and 100 mM citrate-phosphate buffer pH 4.8
Crystal Properties
Matthews coefficientSolvent content
3.3363.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.461α = 90
b = 106.461β = 90
c = 96.116γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.954Australian SynchrotronMX2

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
12.492.2990.0819.716.123081
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.4

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 REPLACEMENTTHROUGHOUT4JZJ, 1JLI2.492.223081124299.720.217630.216330.24199RANDOM70.84
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]
0.480.240.48-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.569
r_dihedral_angle_3_deg16.522
r_dihedral_angle_4_deg16.414
r_dihedral_angle_1_deg6.456
r_long_range_B_refined5.854
r_long_range_B_other5.853
r_mcangle_it3.115
r_mcangle_other3.114
r_scangle_other2.887
r_mcbond_other1.737
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.569
r_dihedral_angle_3_deg16.522
r_dihedral_angle_4_deg16.414
r_dihedral_angle_1_deg6.456
r_long_range_B_refined5.854
r_long_range_B_other5.853
r_mcangle_it3.115
r_mcangle_other3.114
r_scangle_other2.887
r_mcbond_other1.737
r_mcbond_it1.736
r_scbond_it1.632
r_scbond_other1.631
r_angle_refined_deg1.55
r_angle_other_deg0.995
r_chiral_restr0.103
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2958
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing