6TM4

NatL2 in complex with two molecules of salicylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SIW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M KSCN, 0.1 M sodium citrate pH 6, 24-32% PEG MME 2K
Crystal Properties
Matthews coefficientSolvent content
2.5150.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.46α = 90
b = 139.24β = 90
c = 129.66γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.8971.131000.1190.9979.46.577807
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)
11.891.941001.6280.651.36.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6SIW1.8971.12877773381199.9490.1990.19780.230347.313
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]
-2.7323.626-0.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.437
r_dihedral_angle_4_deg21.446
r_dihedral_angle_3_deg14.626
r_dihedral_angle_1_deg6.974
r_lrange_other5.323
r_lrange_it5.322
r_scangle_it3.478
r_scangle_other3.478
r_mcangle_it2.734
r_mcangle_other2.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.437
r_dihedral_angle_4_deg21.446
r_dihedral_angle_3_deg14.626
r_dihedral_angle_1_deg6.974
r_lrange_other5.323
r_lrange_it5.322
r_scangle_it3.478
r_scangle_other3.478
r_mcangle_it2.734
r_mcangle_other2.734
r_scbond_it2.196
r_scbond_other2.195
r_mcbond_it1.795
r_mcbond_other1.792
r_angle_refined_deg1.563
r_angle_other_deg1.306
r_nbd_other0.218
r_symmetry_xyhbond_nbd_refined0.205
r_nbd_refined0.193
r_symmetry_nbd_other0.18
r_symmetry_nbd_refined0.18
r_nbtor_refined0.161
r_xyhbond_nbd_refined0.147
r_ncsr_local_group_10.095
r_symmetry_nbtor_other0.078
r_chiral_restr0.067
r_metal_ion_refined0.056
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6727
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing