8PTE

Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to octadecavanadate ion (structure B)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	20% ethylene glycol, 0.1 M sodium acetate buffer pH 4.0, 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.39	α = 90
b = 80.39	β = 90
c = 36.51	γ = 90

Symmetry
Space Group	P 43 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 6M		2021-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.79	40.19	99.8	0.104	1	33.6	20		11611

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.83	100		1.06	0.912	4.6	15

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	THROUGHOUT	1.797	40.128	11398	580	97.938	0.183	0.1805	0.2325	26.962

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]
-0.219			-0.219		0.438

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.79
r_dihedral_angle_4_deg	18.157
r_dihedral_angle_3_deg	15.367
r_lrange_it	7.157
r_dihedral_angle_1_deg	6.864
r_lrange_other	6.786
r_scangle_other	4.817
r_scangle_it	4.651
r_mcangle_other	3.243
r_mcangle_it	3.23
r_scbond_other	2.995
r_scbond_it	2.974
r_mcbond_it	2.29
r_mcbond_other	2.253
r_angle_refined_deg	2.071
r_angle_other_deg	1.415
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.241
r_metal_ion_refined	0.232
r_xyhbond_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_other	0.188
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.161
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.081
r_symmetry_metal_ion_refined	0.048
r_xyhbond_nbd_other	0.047
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	56

Software

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