9OZ4 | pdb_00009oz4

Crystal Structure of Substrate Binding Protein (TAXI-TRAP) in Complex with L-Glutamate from Bordetella pertussis

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, SITTING DROP	9.5	293.15	0.1 M CHES, 20% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
1.91	41.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.43	α = 90
b = 76.913	β = 93.677
c = 65.233	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		2025-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953732	Australian Synchrotron	MX2

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	2.008	45.998	99.3	0.085	0.101	0.054	0.997	12.3	6.8		37733

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	2.01	2.06			0.546	0.646	0.342	0.954		6.5

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	2.01	45.996	37713	1805	99.357	0.17	0.1648	0.1643	0.2781	0.2769	38.748

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]
-3.719		-4.031	-1.15		5.343

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.918
r_dihedral_angle_3_deg	16.244
r_dihedral_angle_4_deg	16.112
r_lrange_it	9.735
r_lrange_other	9.732
r_rigid_bond_restr	9.529
r_scangle_other	7.984
r_scangle_it	7.983
r_mcangle_it	7.701
r_mcangle_other	7.7
r_dihedral_angle_1_deg	6.772
r_scbond_it	6.573
r_scbond_other	6.568
r_mcbond_it	5.932
r_mcbond_other	5.928
r_angle_refined_deg	1.502
r_angle_other_deg	1.305
r_nbd_other	0.233
r_symmetry_xyhbond_nbd_refined	0.22
r_symmetry_xyhbond_nbd_other	0.211
r_nbd_refined	0.2
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.169
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4534
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
MOLREP	phasing
Coot	model building
Aimless	data scaling
XDS	data reduction