13CZ | pdb_000013cz

Crystal structure of DcrB from Salmonella enterica at pH 5.0

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	5	293.15	0.1 M sodium acetate pH 5.0, 34% (v/v) polyethylene glycol 5,000

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.204	α = 90
b = 37.836	β = 110.128
c = 67.276	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 9M		2025-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.136	37.84	99.74	0.118	0.996	6.97	6.6		14748

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	2.136	2.17	93.35		0.491	0.849	1.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.136	34.671	14738	757	99.642	0.19	0.1876	0.1875	0.2384	0.2385	RANDOM	44.506

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]
-1.952		0.321	0.277		1.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.663
r_dihedral_angle_6_deg	12.949
r_lrange_it	8.739
r_dihedral_angle_2_deg	8.404
r_dihedral_angle_1_deg	6.785
r_scangle_it	6.381
r_mcangle_it	4.221
r_scbond_it	4.114
r_mcbond_it	2.692
r_angle_refined_deg	1.912
r_nbtor_refined	0.274
r_symmetry_nbd_refined	0.193
r_nbd_refined	0.181
r_ncsr_local_group_1	0.151
r_chiral_restr	0.135
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.111
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2270
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms

Software

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