8GI3

Crystal structure of RhoA mutant L69P complexed with GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6V6U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.1293.20.2 M Ammonium citrate dibasic (pH 5.1), 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.048α = 90
b = 64.081β = 90
c = 82.504γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2022-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.5250.6699.70.110.120.0460.98813.16.52685211.25
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)
11.521.5599.70.1430.1540.0580.9810.66.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5250.6626852134199.540.17250.170570.20947RANDOM13.318
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]
-0.05-0.140.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.401
r_dihedral_angle_2_deg7.712
r_dihedral_angle_1_deg5.913
r_long_range_B_refined5.782
r_long_range_B_other5.638
r_scangle_other4.11
r_scbond_other2.74
r_scbond_it2.737
r_mcangle_other2.473
r_mcangle_it2.472
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.401
r_dihedral_angle_2_deg7.712
r_dihedral_angle_1_deg5.913
r_long_range_B_refined5.782
r_long_range_B_other5.638
r_scangle_other4.11
r_scbond_other2.74
r_scbond_it2.737
r_mcangle_other2.473
r_mcangle_it2.472
r_angle_refined_deg1.896
r_mcbond_it1.612
r_mcbond_other1.609
r_angle_other_deg0.635
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1417
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms29

Software

Software
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling