8QUA | pdb_00008qua

GTP binding protein YsxC from Staphylococcus aureus

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	7.2	295.15	2.6M Potassium/sodium phosphate pH 7.6

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.942	α = 90
b = 55.942	β = 90
c = 107.112	γ = 120

Symmetry
Space Group	P 32 2 1

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	RIGAKU HyPix-6000HE		2022-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54184

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	20.05	99.6	0.087	0.098	0.044	0.998	11.3	7.7		13613

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)	Redundancy	Number Unique Reflections (All)
1	2	20.05			0.049	0.054	0.021	0.999		8.3

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	20.046	13539	708	99.245	0.26	0.257	0.26	0.3165	0.31	37.306

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]
2.787			2.787		-5.574

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.973
r_dihedral_angle_3_deg	14.535
r_dihedral_angle_1_deg	9.176
r_dihedral_angle_2_deg	7.999
r_lrange_it	7.775
r_lrange_other	7.773
r_mcangle_it	5.655
r_mcangle_other	5.652
r_scangle_it	4.934
r_scangle_other	4.932
r_mcbond_it	3.953
r_mcbond_other	3.95
r_scbond_it	3.404
r_scbond_other	3.402
r_angle_refined_deg	2.058
r_angle_other_deg	1.008
r_nbd_refined	0.164
r_nbtor_refined	0.141
r_symmetry_nbd_other	0.127
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.119
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbd_refined	0.087
r_nbd_other	0.083
r_symmetry_nbtor_other	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
CrysalisPro	data collection
Coot	model building
PHASER	phasing
CrysalisPro	data reduction
CrysalisPro	data scaling