8X18 | pdb_00008x18

Xanthomonas campestris pv. campestris OpgD mutant-D379N with beta-1,2-glucan

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	5.5	293	Bis-Tris HCl (pH5.5), Ammonium sulfate, glycerol, beta-1,2-glucan

Crystal Properties
Matthews coefficient	Solvent content
4.89	74.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.878	α = 90
b = 171.878	β = 90
c = 128.691	γ = 120

Symmetry
Space Group	P 65

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 S 6M		2023-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.25	48.723	100	0.996	11.6	10.4		102253

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29			0.83

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	2.25	48.723	102207	5213	99.987	0.173	0.1726	0.1807	0.1761	0.1842	31.145

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]
-0.632	-0.316		-0.632		2.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.316
r_dihedral_angle_6_deg	16.14
r_dihedral_angle_3_deg	15.57
r_lrange_other	7.951
r_lrange_it	7.942
r_dihedral_angle_1_deg	6.977
r_scangle_it	6.37
r_scangle_other	6.369
r_mcangle_it	4.377
r_mcangle_other	4.377
r_scbond_it	4.297
r_scbond_other	4.297
r_mcbond_it	3.042
r_mcbond_other	3.042
r_angle_refined_deg	1.508
r_angle_other_deg	0.837
r_nbd_refined	0.409
r_symmetry_nbd_refined	0.235
r_symmetry_nbd_other	0.229
r_nbd_other	0.197
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.044
r_gen_planes_other	0.012
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7947
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	524

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing