7NSW

The structure of the SBP TarP_Csal in complex with coumarate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NRR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72900.2 M MgCl2, 0.1 M Hepes pH 7.0 and 25 % (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.0539.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.17α = 90
b = 119.94β = 90
c = 62.04γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91731DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.6734.2599.60.1140.0499.87.171530
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.7199.41.1450.561.46.1

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-VALUE7NRR1.6734.2571488343499.480.20.19730.251225.282
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]
3.303-1.933-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.476
r_scbond_it21.789
r_scbond_other21.785
r_scangle_it18.288
r_scangle_other18.286
r_dihedral_angle_4_deg16.324
r_lrange_it16.137
r_lrange_other16.136
r_dihedral_angle_3_deg13.922
r_mcbond_it7.996
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.476
r_scbond_it21.789
r_scbond_other21.785
r_scangle_it18.288
r_scangle_other18.286
r_dihedral_angle_4_deg16.324
r_lrange_it16.137
r_lrange_other16.136
r_dihedral_angle_3_deg13.922
r_mcbond_it7.996
r_mcbond_other7.985
r_mcangle_other7.732
r_mcangle_it7.731
r_dihedral_angle_1_deg6.569
r_angle_refined_deg1.643
r_angle_other_deg1.456
r_symmetry_nbd_refined0.243
r_nbd_other0.213
r_nbd_refined0.207
r_symmetry_nbd_other0.18
r_symmetry_xyhbond_nbd_refined0.179
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.152
r_metal_ion_refined0.099
r_chiral_restr0.082
r_symmetry_nbtor_other0.08
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5101
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing