5FNI

Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CQ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.515 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Crystal Properties
Matthews coefficientSolvent content
2.141.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.687α = 90
b = 41.544β = 104.44
c = 72.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2015-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

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
11.641.597.90.0816.77.231958
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)
11.61.6375.80.692.35.4

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 REPLACEMENTTHROUGHOUT4CQ01.669.8130348159697.860.151110.148990.19286RANDOM16.744
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]
-0.23-0.060.070.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.315
r_dihedral_angle_4_deg18.931
r_dihedral_angle_3_deg13.15
r_dihedral_angle_1_deg6.822
r_scbond_it3.393
r_mcangle_it2.759
r_mcbond_it1.977
r_mcbond_other1.971
r_angle_refined_deg1.944
r_angle_other_deg1.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.315
r_dihedral_angle_4_deg18.931
r_dihedral_angle_3_deg13.15
r_dihedral_angle_1_deg6.822
r_scbond_it3.393
r_mcangle_it2.759
r_mcbond_it1.977
r_mcbond_other1.971
r_angle_refined_deg1.944
r_angle_other_deg1.051
r_chiral_restr0.127
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing