X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XNF1XNF, 4QL6
experimental modelPDB 4QL61XNF, 4QL6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42890.2 M Ammonium citrate, 14% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.9558.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.594α = 90
b = 146.726β = 90
c = 148.429γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.20NSRRCBL15A1

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
12.3104.3599.90.0670.95521.054.5105941
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)
12.32.381000.6820.8174.6

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 REPLACEMENTTHROUGHOUT1XNF, 4QL62.3104.35100514547090.30.220.2170.271RANDOM44.84
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]
-0.390.090.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.847
r_dihedral_angle_3_deg23.142
r_dihedral_angle_4_deg22.409
r_long_range_B_refined8.427
r_long_range_B_other8.405
r_scangle_other5.692
r_mcangle_it5.441
r_mcangle_other5.441
r_angle_other_deg3.797
r_scbond_it3.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.847
r_dihedral_angle_3_deg23.142
r_dihedral_angle_4_deg22.409
r_long_range_B_refined8.427
r_long_range_B_other8.405
r_scangle_other5.692
r_mcangle_it5.441
r_mcangle_other5.441
r_angle_other_deg3.797
r_scbond_it3.631
r_scbond_other3.63
r_mcbond_it3.604
r_mcbond_other3.602
r_dihedral_angle_1_deg2.703
r_angle_refined_deg1.774
r_chiral_restr0.193
r_bond_refined_d0.026
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_bond_other_d
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 Atoms14758
Nucleic Acid Atoms
Solvent Atoms946
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
Cootmodel building
HKL-2000data scaling