9GOG | pdb_00009gog

X-ray structure of lysozyme obtained upon reaction with the dioxidovanadium(V) complex with furan-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	4	293	1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.846	α = 90
b = 76.846	β = 90
c = 36.839	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 EIGER2 S 16M		2023-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	1.24	54.34	100	0.999	15	20		32110

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	1.24	1.26			0.412

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	1.24	54.338	31754	1554	99.689	0.205	0.203	0.2129	0.2559	0.2642	24.679

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]
0.095			0.095		-0.191

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.222
r_dihedral_angle_4_deg	19.309
r_dihedral_angle_3_deg	14.953
r_dihedral_angle_1_deg	6.696
r_lrange_it	5.677
r_lrange_other	5.446
r_scangle_it	4.295
r_scangle_other	4.191
r_mcangle_it	2.96
r_mcangle_other	2.958
r_scbond_it	2.728
r_scbond_other	2.638
r_mcbond_it	2.159
r_mcbond_other	2.157
r_angle_refined_deg	1.86
r_angle_other_deg	1.541
r_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.249
r_xyhbond_nbd_refined	0.235
r_nbd_other	0.221
r_symmetry_nbd_refined	0.213
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.18
r_metal_ion_refined	0.131
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	60

Software

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