7ZU6

Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to tetra-vanadate ion (structure 1)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.0 M sodium formate 0.1 M hepes buffer pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.05	α = 90
b = 77.05	β = 90
c = 37.84	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 PILATUS 6M		2022-03-04	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	1.18	38.52	99.9	0.055	0.999	24.1	18		37733

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	1.18	1.2	100		0.872	0.847	2.3	8.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	193l	1.183	38.52	36335	1755	96.285	0.172	0.1707	0.1961	18.152

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]
-0.004			-0.004		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.526
r_dihedral_angle_4_deg	18.277
r_dihedral_angle_3_deg	15.321
r_dihedral_angle_1_deg	6.473
r_lrange_it	5.991
r_lrange_other	5.792
r_scangle_it	4.226
r_scangle_other	4.166
r_scbond_it	2.784
r_scbond_other	2.723
r_mcangle_other	2.141
r_mcangle_it	2.134
r_angle_refined_deg	2.095
r_angle_other_deg	1.644
r_mcbond_it	1.435
r_mcbond_other	1.423
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_other	0.206
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.113
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.083
r_xyhbond_nbd_other	0.054
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
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	178
Heterogen Atoms	35

Software

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