6X1G

Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FOE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH9.529325 mM CHES pH 9.5, 25% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.063α = 83.37
b = 54.16β = 76.34
c = 94.004γ = 62.52
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.98APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.65081.70.0380.0530.03810.41.692107
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6380.20.7311.0330.7310.2951.6

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 REPLACEMENTTHROUGHOUT1FOE1.648.0587425466381.520.18280.1810.2182RANDOM45.588
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]
0.140.29-0.22-0.37-0.050.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.414
r_dihedral_angle_4_deg18.482
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg6.023
r_angle_refined_deg1.808
r_angle_other_deg1.517
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.414
r_dihedral_angle_4_deg18.482
r_dihedral_angle_3_deg14.429
r_dihedral_angle_1_deg6.023
r_angle_refined_deg1.808
r_angle_other_deg1.517
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6266
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing