5ZHX

Crystal structure of SmgGDS-558 and farnesylated RhoA complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2830.2M Sodium malonate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9958.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.32α = 90
b = 181.77β = 90
c = 205.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.5136.199.910.443.844892132.227
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.59

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT3.5136.142482221399.630.252780.249940.30625RANDOM
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]
-0.420.130.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.512
r_dihedral_angle_3_deg20.881
r_long_range_B_refined17.011
r_long_range_B_other17.011
r_dihedral_angle_4_deg14.087
r_scangle_other11.804
r_mcangle_it11.451
r_mcangle_other11.45
r_dihedral_angle_1_deg7.69
r_scbond_it6.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.512
r_dihedral_angle_3_deg20.881
r_long_range_B_refined17.011
r_long_range_B_other17.011
r_dihedral_angle_4_deg14.087
r_scangle_other11.804
r_mcangle_it11.451
r_mcangle_other11.45
r_dihedral_angle_1_deg7.69
r_scbond_it6.991
r_scbond_other6.991
r_mcbond_it6.929
r_mcbond_other6.929
r_angle_refined_deg1.42
r_angle_other_deg1.153
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms18728
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing