9X3C | pdb_00009x3c

Crystal structure of B. subtilis YdzF in reduced 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		298	Protein buffer: 50 mM HEPES-Na, pH 7.5, 100 mM NaCl, 5% (v/v) glycerol, and 0.1 mM TCEP. Crystallization solution: 100 mM Sodium acetate trihydrate, pH 4.6, 2.0 M Sodium formate. Protein and crystallization solution were mixed in a 1:1 ratio (microbatch under 1:1 paraffin oil to silicon oil).

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.07	α = 90
b = 119.03	β = 90
c = 79.92	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		2023-11-10	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	2.54	41.95	98.6	0.082	0.1	0.055	0.989	7.3	3.04		18602			36.15

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	2.54	2.65	97.8		0.404	0.488	0.269	0.575	2.5	3.07

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	2.54	41.95	18602	1025	98.195	0.246	0.2426	0.2452	0.3084	0.3117	47.365

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]
2.235			0.856		-3.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.666
r_dihedral_angle_6_deg	17.611
r_lrange_it	17.549
r_lrange_other	17.523
r_dihedral_angle_3_deg	15.59
r_scangle_it	13.748
r_scangle_other	13.745
r_mcangle_it	13.086
r_mcangle_other	13.085
r_scbond_it	9.432
r_scbond_other	9.431
r_mcbond_it	8.166
r_mcbond_other	8.156
r_rigid_bond_restr	6.431
r_dihedral_angle_1_deg	5.907
r_angle_refined_deg	1.952
r_angle_other_deg	0.624
r_symmetry_nbd_refined	0.311
r_nbd_other	0.268
r_nbd_refined	0.243
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.139
r_ncsr_local_group_3	0.114
r_ncsr_local_group_1	0.11
r_ncsr_local_group_4	0.104
r_ncsr_local_group_6	0.098
r_ncsr_local_group_2	0.094
r_ncsr_local_group_5	0.091
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2757
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms

Software

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