8CC5

Vibrio cholerae GbpA (LPMO domain)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XWX	Truncated after residue 203

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Zinc Acetate 0.1 M Sodium Cacodylate pH 6.5 18% w/v PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.333	α = 90
b = 89.374	β = 90
c = 47.497	γ = 90

Symmetry
Space Group	P 21 21 2

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 2M		2021-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.87313	ESRF	ID23-1

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	1.62	47.542	99.94	0.998	10.83	6.8		78744

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	1.62	1.68			0.374

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.62	47.542	41528	2034	99.966	0.178	0.1763	0.213	25.413

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]
-1.884			0.881		1.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.756
r_dihedral_angle_3_deg	14.295
r_lrange_other	8.791
r_lrange_it	8.784
r_dihedral_angle_1_deg	8.297
r_scangle_it	7.199
r_scangle_other	7.198
r_dihedral_angle_2_deg	6.085
r_scbond_it	4.998
r_scbond_other	4.997
r_mcangle_it	4.32
r_mcangle_other	4.319
r_mcbond_it	3.409
r_mcbond_other	3.326
r_angle_refined_deg	1.341
r_angle_other_deg	0.461
r_symmetry_nbd_refined	0.354
r_nbd_other	0.32
r_nbd_refined	0.228
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.126
r_symmetry_metal_ion_refined	0.125
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.061
r_gen_planes_refined	0.016
r_bond_refined_d	0.006
r_gen_planes_other	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing