X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Protein stock of RhoA-Y34F3Y 0.7 mM, RhoGAP-R85A 0.7 mM in a buffer of BisTris-HCl, pH 6.0, NaCl 150 mM, MgCl2 5 mM, NaF 10 mM, DTT 1 mM mixed 1:1.2 ratio with the precipitant solution of 0.1 M BisTris-HCl, pH 5.8, PEG3350 26% (w/v).
Crystal Properties
Matthews coefficientSolvent content
1.9336.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.765α = 90
b = 66.489β = 95.27
c = 76.958γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9155.641000.1350.160.0850.99610.46.757691
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)
11.911.951000.6491

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5M6X1.9155.6454747291899.970.24620.24360.2945RANDOM28.051
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]
2.80.89-2.71-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg18.928
r_dihedral_angle_3_deg15.55
r_dihedral_angle_1_deg6.207
r_angle_refined_deg1.351
r_angle_other_deg1.161
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg18.928
r_dihedral_angle_3_deg15.55
r_dihedral_angle_1_deg6.207
r_angle_refined_deg1.351
r_angle_other_deg1.161
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5847
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing