9EX0 | pdb_00009ex0

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure A)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	1.1 M NaCl, 0.1 M sodium acetate at pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.55	α = 90
b = 80.55	β = 90
c = 36.28	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		2023-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	1.45	56.96	99.8	0.085	0.088	0.024	0.999	16.8	14.2		21715

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	1.45	1.47	100		1.199	1.241	0.318	0.831		14.8

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	1.45	56.957	21093	1057	97.042	0.197	0.1956	0.2	0.2189	0.23	16.855

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]
-0.068			-0.068		0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.863
r_dihedral_angle_3_deg	15.647
r_dihedral_angle_2_deg	11.978
r_dihedral_angle_1_deg	6.955
r_lrange_other	6.034
r_lrange_it	6.031
r_scangle_other	4.137
r_scangle_it	4.124
r_scbond_it	2.733
r_scbond_other	2.644
r_mcangle_other	2.334
r_mcangle_it	2.33
r_angle_refined_deg	1.691
r_mcbond_it	1.558
r_mcbond_other	1.496
r_angle_other_deg	0.585
r_xyhbond_nbd_refined	0.375
r_symmetry_nbd_refined	0.309
r_nbd_refined	0.259
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.155
r_chiral_restr	0.086
r_nbd_other	0.086
r_symmetry_nbtor_other	0.081
r_symmetry_metal_ion_refined	0.064
r_metal_ion_refined	0.04
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	45

Software

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