9I0E | pdb_00009i0e

Crystal structure of the non-heme domain from PgcA - Wildtype

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	8.5	289.15	0.3 uL of protein solution, 0.28 uL of 1.5 M ammonium sulfate, 12 % v/v glycerol, 100 mM Tris-HCl pH 8.5, and 0.02 uL of 10 % w/v PEG 8000, 8 % v/v ethylene glycol, 100 mM HEPES pH 7.5 equilibrated against 50 uL buffer D mother liquor.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.756	α = 90
b = 96.756	β = 90
c = 35.916	γ = 120

Symmetry
Space Group	P 61

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 PILATUS3 6M		2024-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9537	Diamond	I24

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	1.65	83.79	100	0.038	0.039	0.009	1	56.1	18.7		23436

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	1.65	1.68		100	0.119	0.125	0.038	0.994		10.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	41.9	1.47	23416	1161	100	0.1668	0.1656	0.1663	0.1904	0.1912

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.776
f_angle_d	1.048
f_chiral_restr	0.065
f_bond_d	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1395
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	21

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing