9JKP | pdb_00009jkp

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	295.15	0.228M tri-Potassium citrate pH 8.3, 25% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
5.44	77.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.146	α = 90
b = 78.146	β = 90
c = 244.905	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 2M		2024-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.977	LNLS SIRIUS	MANACA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.76	48.2	99.5	0.025	0.036	0.025	1	15.3	2		20362

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)	Redundancy	Number Unique Reflections (All)
1	2.76	2.86	94.7		1.037	0.417	0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.76	48.195	20348	1018	99.569	0.173	0.1698	0.1698	0.2236	0.2234	98.104

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			-3.498		6.996

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	35.594
r_lrange_other	35.582
r_scangle_it	29.524
r_scangle_other	29.516
r_mcangle_other	28.864
r_mcangle_it	28.861
r_scbond_it	20.083
r_scbond_other	20.065
r_mcbond_it	19.715
r_mcbond_other	19.707
r_dihedral_angle_3_deg	17.819
r_dihedral_angle_2_deg	14.724
r_dihedral_angle_6_deg	14.595
r_dihedral_angle_1_deg	10.179
r_rigid_bond_restr	4.918
r_angle_refined_deg	2.57
r_angle_other_deg	1.29
r_dihedral_angle_other_2_deg	0.538
r_nbd_refined	0.14
r_chiral_restr	0.136
r_nbtor_refined	0.131
r_symmetry_nbd_other	0.103
r_symmetry_xyhbond_nbd_refined	0.09
r_nbd_other	0.082
r_xyhbond_nbd_refined	0.072
r_symmetry_nbtor_other	0.06
r_symmetry_nbd_refined	0.053
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2404
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Coot	model building