9RD1 | pdb_00009rd1

OppA from E. coli in complex with GSisoK

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TCF	Crystal structure of E. coli OppA complexed with endogenous ligands

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	15% Ethanol, 40% Pentaerythritol propoxylate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.99	α = 90
b = 200.69	β = 95.73
c = 103.38	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	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.0597	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	30	95.8	0.119	7.5	3.1		80198

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	99.6		0.688	2	3.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	30	76162	4008	95.73	0.23142	0.22936	0.2407	0.2593	0.2679	RANDOM	34.5

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]
5.32		0.08	-2.18		-3.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.495
r_dihedral_angle_3_deg	15.488
r_dihedral_angle_4_deg	14.81
r_dihedral_angle_1_deg	5.735
r_long_range_B_refined	1.476
r_long_range_B_other	1.474
r_angle_refined_deg	1.193
r_angle_other_deg	1.091
r_mcangle_it	0.989
r_mcangle_other	0.989
r_scangle_other	0.859
r_mcbond_it	0.686
r_mcbond_other	0.685
r_scbond_other	0.591
r_scbond_it	0.59
r_rigid_bond_restr	0.23
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16492
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	104

Software

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