7S0Z | pdb_00007s0z

Structures of TcdB in complex with R-Ras


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6OQ76OQ7,2FN4
experimental modelPDB 2FN46OQ7,2FN4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate, pH 4.8, and 17% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.6252.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.308α = 90
b = 112.112β = 95.89
c = 101.571γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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
12.34112.1198.90.0850.9939.63.470923
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.390.693

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6OQ7,2FN42.3476.0267379351698.80.2030.2010.20.2410.24RANDOM37.61
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]
1.821.94-2.03-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg20.044
r_dihedral_angle_3_deg17.422
r_dihedral_angle_1_deg6.181
r_long_range_B_refined3.827
r_long_range_B_other3.804
r_scangle_other2.5
r_mcangle_it2.17
r_mcangle_other2.17
r_scbond_other1.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg20.044
r_dihedral_angle_3_deg17.422
r_dihedral_angle_1_deg6.181
r_long_range_B_refined3.827
r_long_range_B_other3.804
r_scangle_other2.5
r_mcangle_it2.17
r_mcangle_other2.17
r_scbond_other1.538
r_scbond_it1.537
r_angle_other_deg1.459
r_mcbond_it1.306
r_mcbond_other1.306
r_angle_refined_deg1.23
r_chiral_restr0.062
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms11614
Nucleic Acid Atoms
Solvent Atoms539
Heterogen Atoms265

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing