9S2A | pdb_00009s2a

X-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with thiophene-2-carboxylic acid (3-ethoxy-2-hydroxybenzylidene)hydrazide

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		293	1.1 M sodium chloride, 0.1 M sodium acetate at pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.57	α = 90
b = 76.57	β = 90
c = 36.73	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		2024-06-04	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)	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	1.31	38.29	91.1	0.999	13.3	22.4		24505

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	1.31	1.33			0.326

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	1.37	38.29	20294	1003	86.368	0.197	0.1951	0.202	0.233	0.2379	27.59

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]
-0.099			-0.099		0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.981
r_dihedral_angle_4_deg	27.219
r_dihedral_angle_3_deg	15.603
r_lrange_it	7.578
r_lrange_other	7.193
r_dihedral_angle_1_deg	6.626
r_scangle_it	5.093
r_scangle_other	5.06
r_mcangle_other	3.533
r_mcangle_it	3.513
r_scbond_it	3.303
r_scbond_other	3.217
r_mcbond_it	2.461
r_mcbond_other	2.412
r_angle_refined_deg	1.817
r_angle_other_deg	1.569
r_nbd_refined	0.236
r_nbd_other	0.224
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.188
r_xyhbond_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.185
r_metal_ion_refined	0.174
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
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	81
Heterogen Atoms	49

Software

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