8RP7 | pdb_00008rp7

Glutaminase subunit of aminodeoxychorismate synthase from Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P00903-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	sodium formate, PEG3350, L-glutamine

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.784	α = 90
b = 115.582	β = 101.062
c = 63.538	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976200	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.82	42.423	98.54	0.3132	0.984	6.84	5.1		12448

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	2.82	2.921	98.31		1.486	0.513	1.75	5.1

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	2.82	42.423	12431	638	98.698	0.214	0.2109	0.2135	0.2679	0.2711	51.505

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]
0.186		1.105	-1.185		0.527

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.6
r_dihedral_angle_4_deg	20.949
r_dihedral_angle_3_deg	20.864
r_lrange_it	11.96
r_lrange_other	11.96
r_dihedral_angle_1_deg	6.751
r_scangle_it	4.478
r_scangle_other	4.478
r_mcangle_other	4.477
r_mcangle_it	4.474
r_scbond_it	2.599
r_scbond_other	2.597
r_mcbond_it	2.582
r_mcbond_other	2.571
r_angle_refined_deg	1.405
r_angle_other_deg	1.387
r_symmetry_xyhbond_nbd_refined	0.38
r_nbd_other	0.309
r_symmetry_nbd_refined	0.294
r_nbd_refined	0.217
r_symmetry_nbd_other	0.213
r_ncsr_local_group_3	0.18
r_symmetry_xyhbond_nbd_other	0.173
r_nbtor_refined	0.171
r_ncsr_local_group_2	0.17
r_ncsr_local_group_1	0.15
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4413
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing