9WVG | pdb_00009wvg

Crystal structure of B. subtilis YdzF in oxidized state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-O31494-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	298	Protein buffer: 50 mM HEPES-Na, pH 7.5, 100 mM NaCl, 5% (v/v) glycerol. Crystallization solution: 200 mM sodium citrate tribasic dihydrate, 100 mM HEPES-Na, pH 7.5, 30% (v/v) (+/-)-2-methyl-2,4-pentanediol (MPD). Protein and crystallization solution were mixed 1:1 (microbatch under 1:1 paraffin oil to silicon oil).

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.43	α = 90
b = 118.5	β = 90
c = 80.24	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2023-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54179

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	2.26	57.83	98.7	0.079	0.098	0.056	0.995	5.7	2.83		25498			37.3

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	2.26	2.35	97		0.405	0.501	0.292	0.309	2.5	2.75

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	2.262	41.706	25490	1234	96.134	0.226	0.2238	0.2337	0.276	0.2913	47.612

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]
18.307			7.861		-26.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.397
r_lrange_it	22.887
r_lrange_other	22.887
r_dihedral_angle_3_deg	19.715
r_dihedral_angle_6_deg	16.099
r_scangle_it	14.774
r_scangle_other	14.771
r_mcangle_it	13.111
r_mcangle_other	13.108
r_scbond_it	10.188
r_scbond_other	10.185
r_mcbond_it	8.42
r_mcbond_other	8.417
r_rigid_bond_restr	7.076
r_dihedral_angle_1_deg	4.271
r_angle_refined_deg	1.637
r_angle_other_deg	0.569
r_symmetry_xyhbond_nbd_refined	0.38
r_nbd_other	0.315
r_symmetry_nbd_refined	0.302
r_nbd_refined	0.245
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.196
r_ncsr_local_group_6	0.183
r_ncsr_local_group_3	0.178
r_ncsr_local_group_5	0.174
r_ncsr_local_group_1	0.167
r_ncsr_local_group_2	0.165
r_ncsr_local_group_4	0.159
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2927
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	12

Software

Software
Software Name	Purpose
Coot	model building
REFMAC	refinement
PHASER	phasing
PARROT	phasing
Aimless	data scaling
iMOSFLM	data reduction
MAR345dtb	data collection