9JKP | pdb_00009jkp

Crystal structure of the Staphylococcus aureus GTPase Era in complex with GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3295.150.228M tri-Potassium citrate pH 8.3, 25% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
5.4477.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.146α = 90
b = 78.146β = 90
c = 244.905γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 2M2024-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS SIRIUS BEAMLINE MANACA0.977LNLS SIRIUSMANACA

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
12.7648.299.50.0250.0360.025115.3220362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.762.8694.71.0370.4170.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.7648.19520348101899.5690.1730.16980.16980.22360.223498.104
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]
-3.498-3.4986.996
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it35.594
r_lrange_other35.582
r_scangle_it29.524
r_scangle_other29.516
r_mcangle_other28.864
r_mcangle_it28.861
r_scbond_it20.083
r_scbond_other20.065
r_mcbond_it19.715
r_mcbond_other19.707
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it35.594
r_lrange_other35.582
r_scangle_it29.524
r_scangle_other29.516
r_mcangle_other28.864
r_mcangle_it28.861
r_scbond_it20.083
r_scbond_other20.065
r_mcbond_it19.715
r_mcbond_other19.707
r_dihedral_angle_3_deg17.819
r_dihedral_angle_2_deg14.724
r_dihedral_angle_6_deg14.595
r_dihedral_angle_1_deg10.179
r_rigid_bond_restr4.918
r_angle_refined_deg2.57
r_angle_other_deg1.29
r_dihedral_angle_other_2_deg0.538
r_nbd_refined0.14
r_chiral_restr0.136
r_nbtor_refined0.131
r_symmetry_nbd_other0.103
r_symmetry_xyhbond_nbd_refined0.09
r_nbd_other0.082
r_xyhbond_nbd_refined0.072
r_symmetry_nbtor_other0.06
r_symmetry_nbd_refined0.053
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
Cootmodel building