9I8L | pdb_00009i8l

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2</sub>] at 310 K

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	310	1,1 M sodium chloride and 0,1 M sodium acetate buffer pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.86	α = 90
b = 80.86	β = 90
c = 36.83	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	310	PIXEL	DECTRIS PILATUS 6M		2024-11-20	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)	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	1.83	57.177	90	0.116	0.997	8.9	8.7		10096

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	1.83	1.86	100		6.402	0.369	0.3	8.8

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	1.831	57.177	8732	428	77.721	0.205	0.2001	0.207	0.2838	0.292	40.129

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]
-0.389			-0.389		0.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.956
r_dihedral_angle_3_deg	15.382
r_lrange_it	9.008
r_lrange_other	8.892
r_dihedral_angle_2_deg	8.367
r_dihedral_angle_1_deg	7.519
r_scangle_other	5.848
r_scangle_it	5.651
r_scbond_it	4.563
r_mcangle_other	4.092
r_mcangle_it	4.091
r_scbond_other	3.955
r_mcbond_it	3.159
r_mcbond_other	3.118
r_angle_refined_deg	1.847
r_angle_other_deg	0.469
r_xyhbond_nbd_refined	0.425
r_symmetry_nbd_refined	0.312
r_symmetry_metal_ion_refined	0.285
r_nbd_refined	0.267
r_nbd_other	0.212
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.209
r_nbtor_refined	0.181
r_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	86

Software

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