7NTD

The structure of the SBP TarP_Csal in complex with ferulate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52900.2 M MgCl2, 0.1 M Tris pH 8.5 and 20 % (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.86α = 101.68
b = 52.28β = 98.59
c = 68.53γ = 104.9
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.7548.8996.80.080.0730.9886.2262516
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.895.40.6870.620.472

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-VALUE7NSW1.7547.12462507304796.8220.1940.19120.251733.081
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]
-1.778-0.730.4430.8950.5430.474
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it32.707
r_scbond_other32.706
r_dihedral_angle_2_deg30.665
r_scangle_it24.544
r_scangle_other24.504
r_lrange_it23.341
r_lrange_other23.339
r_dihedral_angle_4_deg16.312
r_mcbond_it15.085
r_mcbond_other15.069
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it32.707
r_scbond_other32.706
r_dihedral_angle_2_deg30.665
r_scangle_it24.544
r_scangle_other24.504
r_lrange_it23.341
r_lrange_other23.339
r_dihedral_angle_4_deg16.312
r_mcbond_it15.085
r_mcbond_other15.069
r_mcangle_it14.338
r_mcangle_other14.336
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg6.647
r_angle_refined_deg1.458
r_angle_other_deg1.328
r_symmetry_nbd_refined0.205
r_nbd_refined0.199
r_nbd_other0.188
r_symmetry_nbd_other0.176
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.157
r_symmetry_xyhbond_nbd_refined0.142
r_metal_ion_refined0.101
r_symmetry_nbtor_other0.078
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_symmetry_xyhbond_nbd_other0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5006
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing