8CC3 | pdb_00008cc3

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	Residues 24-203

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
1.98	38.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.911	α = 90
b = 89.103	β = 90
c = 47.135	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 PILATUS 6M		2020-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97626	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	1.128	47.14	98.74	0.995	6.13	2.2		221328

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	1.13	1.17			0.219

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	1.128	47.135	117455	5893	98.558	0.175	0.1735	0.18	0.2007	0.21	11.934

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]
-1.256			-1.578		2.834

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.038
r_dihedral_angle_3_deg	13.27
r_dihedral_angle_1_deg	7.69
r_dihedral_angle_2_deg	7.286
r_rigid_bond_restr	5.639
r_lrange_it	2.37
r_lrange_other	2.267
r_scangle_it	1.69
r_scangle_other	1.689
r_angle_refined_deg	1.504
r_mcangle_it	1.471
r_mcangle_other	1.471
r_scbond_it	1.277
r_scbond_other	1.276
r_mcbond_it	1.105
r_mcbond_other	1.07
r_angle_other_deg	0.508
r_symmetry_nbd_refined	0.432
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_other	0.242
r_nbd_refined	0.22
r_symmetry_nbd_other	0.213
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.088
r_metal_ion_refined	0.086
r_chiral_restr	0.075
r_symmetry_metal_ion_refined	0.075
r_xyhbond_nbd_other	0.052
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	18

Software

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